CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Application Ser. No. 61/379,630, filed Sep. 2, 2010. The disclosure of the prior application is considered part of (and is incorporated by reference in) the disclosure of this application.
STATEMENT AS TO FEDERALLY SPONSORED RESEARCH Funding for the work described herein was provided by the federal government under grant number HL083141 awarded by the National Heart, Lung, and Blood Institute. The federal government has certain rights in the invention.
BACKGROUND 1. Technical Field
This document relates to methods and materials involved in assessing a mammal (e.g., a human) for a susceptibility to develop venous thromboembolism. For example, this document provides methods and materials for using a genetic variation in an ABO nucleic acid (e.g., rs2519093) to assess an individual's risk for developing venous thromboembolism.
2. Background Information
Venous thromboembolism can present as a deep vein thrombosis (e.g., a blood clot occluding the lumen of large veins) or a pulmonary embolism (e.g., a dislodged deep vein thrombosis that embolized and obstructed one or more arteries to the lung). Venous thromboembolism is a frequent disease with an annual incidence of about 1 per 1000 in the general population (Heit, Arteriosclerosis, Thrombosis and Vascular Biology, 28(3):370-2 (2008)). Venous thromboembolism is responsible for a substantial public health burden, with an estimated one-week mortality rate resulting from disease of about 4% in patients with deep vein thrombosis and 30% in patients with pulmonary embolism (Heit et al., Arch. Intern. Med., 159:445-53 (1999)).
SUMMARY This document provides methods and materials involved in assessing a mammal (e.g., a human) for a susceptibility to develop venous thromboembolism. For example, this document provides methods and materials for using a genetic variation in an ABO nucleic acid (e.g., rs2519093) to assess an individual's risk for developing venous thromboembolism. Having the ability to identify a mammal (e.g., a human) as being likely to develop a venous thromboembolism can allow clinicians to alert patients to their risk and direct those patients to perform certain activities to reduce the likelihood of developing venous thromboembolism. For example, a person identified as having a susceptibility to develop venous thromboembolism based on a genetic analysis provided herein (e.g., the presence of a genetic variation in an ABO nucleic acid such as rs2519093) can be instructed to (a) perform active movements (e.g., move their legs often or take a walk during long plane trips, car trips, and other situations in which they are sitting or lying down for long periods of time), (b) undergo heparin prophylaxis (e.g., low doses of heparin injected under the skin), and/or (c) wear clothes items that provide intermittent pneumatic compression (e.g., soft boots that automatically and gently squeeze the calves periodically).
In general, one aspect of this document features a method for identifying a mammal having increased susceptibility to develop venous thromboembolism. The method comprises, or consists essentially of, (a) determining whether or not a mammal contains a T allele of rs2519093, and (b) classifying the mammal as having an increased susceptibility to develop venous thromboembolism if the mammal contains the T allele. The mammal can be a human. The method can comprise determining whether or not the mammal is heterozygous for the T allele, wherein the mammal has an increased susceptibility to develop venous thromboembolism if the mammal is heterozygous for the T allele. The method can comprise determining whether or not the mammal is homozygous for the T allele, wherein the mammal has an increased susceptibility to develop venous thromboembolism if the mammal is homozygous for the T allele. The method can comprise determining whether or not the mammal contains a G allele of rs6025, a G allele of rs1799963, or a mutant allele of rs8176719.
In another aspect, this document features a method for identifying a mammal having increased susceptibility to develop venous thromboembolism. The method comprises, or consists essentially of, (a) detecting the presence of a mutant T allele of rs2519093 in a mammal, and (b) classifying the mammal as having an increased susceptibility to develop venous thromboembolism based at least in part on the presence of the mutant T allele. The mammal can be a human. The method can comprise determining that the mammal is heterozygous for the mutant T allele. The method can comprise determining that the mammal is homozygous for the mutant T allele. The method can comprise detecting the presence of a G allele of rs6025, a G allele of rs1799963, or a mutant allele of rs8176719.
In another aspect, this document features a method for identifying a mammal having increased susceptibility to develop venous thromboembolism. The method comprises, or consists essentially of, (a) detecting the presence of a mutant T allele of rs2519093 in a mammal, (b) detecting the presence of a G allele of rs6025, a G allele of rs1799963, or a mutant allele of rs8176719, and (c) classifying the mammal as having an increased susceptibility to develop venous thromboembolism based at least in part on the presence of the mutant T allele and the presence of the G allele of rs6025, the G allele of rs1799963, or the mutant allele of rs8176719. The mammal can be a human. The method can comprise determining that the mammal is heterozygous for the mutant T allele. The method can comprise determining that the mammal is homozygous for the mutant T allele.
In another aspect, this document features a method for identifying a mammal having increased susceptibility to develop venous thromboembolism. The method comprises, or consists essentially of, (a) determining whether or not a mammal contains as allele of rs3087505, rs4253399, rs3917862, rs5759224, rs1073897, rs9328375, rs7538157, rs16861990, rs2038024, rs495828, or rs8176719 that is associated with a susceptibility to develop venous thromboembolism, and (b) classifying the mammal as having an increased susceptibility to develop venous thromboembolism if the mammal contains the allele.
In another aspect, this document features a method for identifying a mammal having increased susceptibility to develop venous thromboembolism. The method comprises, or consists essentially of, (a) detecting the presence of, in a mammal, an allele of rs3087505, rs4253399, rs3917862, rs5759224, rs1073897, rs9328375, rs7538157, rs16861990, rs2038024, rs495828, or rs8176719 that is associated with a susceptibility to develop venous thromboembolism, and (b) classifying the mammal as having an increased susceptibility to develop venous thromboembolism based at least in part on the presence of the mutant T allele.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.
Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.
DESCRIPTION OF DRAWINGS FIG. 1 is a table listing the demographic and clinical characteristics by case-control status for a study provided herein.
FIG. 2 is a table listing the number of haplotype bins and single nucleotide polymorphisms (SNPs) after Illumina Infinium Custom genotyping SNP selection, design, manufacture, and assay by pathway.
FIG. 3 contains a graph plotting Multidimensional Scaling using ancestry-informative markers by venous thromboembolism case-control status (top), and by race (bottom).
FIG. 4 is a volcano plot showing each candidate gene SNP by each SNP-specific Odds Ratio and −log10(P-value).
FIG. 5 is a Manhattan plot showing each candidate gene SNP by each SNP-specific chromosome location and −log10(P-value).
FIG. 6 is a haploview plot of the ABO gene. The blocks represent the significant associated SNPs. The first three SNPs within haplotype block 1 indicate ABO blood group SNPs (homozygous deletion of rs8176719 determines 0 blood type), while the second, third, fourth and seventh SNP within haplotype block 2 also are associated with VTE but do not determine ABO blood group.
FIG. 7 is a table of the individual and joint population-attributable risks (AR) for significant SNPs assuming a dominant genetic model for each SNP.
FIG. 8 is a table of a comparison between genotyped and serologic blood type.
FIG. 9 is a table of logistic regression results from genotyped and serologic blood type.
FIG. 10 contains multidimensional scaling plots using the 508 ancestry informative markers for cases and controls (A) and by race (B).
FIG. 11. Association results between VTE and the candidate SNPs using Manhattan plot. The x-axis displays the chromosomes, and y-axis displays the −log10 p-values. The significant results (p-value<10E-4) are labeled by gene name and SNP rs number.
FIG. 12. Haploview linkage disequilibrium plot from ABO gene using the candidate SNPs (n=17). Blocks represent SNPs in high linkage disequilibrium. Greater intensity corresponds to a higher level of linkage disequilibrium given by D′. The value inside each cell represents linkage disequilibrium given by r2. Larger rectangle on the right outlines the ABO blood group SNPs (homozygous deletion on rs8176719 determines O blood type). Smaller rectangles outline the additional significant SNPs in the ABO gene. Display of the ABO SNPs from HapMap build 36.3 is above the Haploview plot.
FIG. 13 contains Q-Q plots under different models indicated by the plot titles.
FIG. 14 is a STRUCTURE triangle plot of 2962 study individuals and 209 unrelated individuals from HapMap Phase II populations (YRI, CEU, and CHB/JPT) using 494 ancestry informative markers.
FIG. 15A is a Manhattan plot of −log10 (P values) from the case-control association analysis on the merged/imputed VTE data assuming an additive genetic model. The top horizontal line represents the Bonferroni correction. The bottom horizontal line represents SNPs exceeding p=−E-05 in Table 11. FIG. 15B is a plot of the location and linkage disequilibrium for SNPs on chromosome 1q surrounding F5. The top triangle corresponds to F5 6025 (Factor V Leiden) the most significant SNP. FIG. 15C is a plot of the location and linkage disequilibrium for SNPs on chromosome 9q surrounding ABO. The top triangle corresponds to the most significant SNP, rs495828.
FIG. 16A provides the odds ratios and 95% confidence intervals around SNPs significantly associated with VTE for genes within chromosome 1.q. FIG. 16B provides the odds ratios and 95% confidence intervals around SNPs significantly associated with VTE for ABO in chromosome 9.
DETAILED DESCRIPTION This document provides methods and materials related to determining whether or not a mammal contains zero, one, or two copies of the T allele of rs2519093. For example, this document provides methods and materials for determining whether or not a mammal is homozygous or heterozygous for the T allele of rs2519093. As described herein, a mammal (e.g., a human) that contains one or two T alleles of rs2519093 can be identified as being likely to develop venous thromboembolism.
The SNP position of rs2519093 is located in the intron 1 region of the ABO blood group nucleic acid (e.g., GenBank® Accession No. NM—020469.2; GI No.: 58331215).
The methods and materials provided herein can be used to determine whether or not nucleic acid of a mammal (e.g., human) contains the T allele of rs2519093. In some cases, the methods and materials provided herein can be used to determine whether both alleles of a mammal contain the T allele of rs2519093, or whether only a single allele of the mammal contains the T allele of rs2519093. The identification of the T allele of rs2519093 can be used to classify or diagnose the mammal as being likely to develop venous thromboembolism. In some cases, a human who has two T alleles at rs2519093 (i.e., a homozygous carrier) can be at higher risk for venous thromboembolism than a human who has one T allele at rs2519093 (i.e., a heterozygous carrier).
Any appropriate method can be used to detect the T allele of rs2519093. For example, mutations can be detected by sequencing cDNA, untranslated sequences, denaturing high performance liquid chromatography (DHPLC; Underhill et al., Genome Res., 7:996-1005 (1997)), allele-specific hybridization (Stoneking et al., Am. J. Hum. Genet., 48:370-382 (1991); and Prince et al., Genome Res., 11(1):152-162 (2001)), allele-specific restriction digests, mutation specific polymerase chain reactions, single-stranded conformational polymorphism detection (Schafer et al., Nat. Biotechnol., 15:33-39 (1998)), infrared matrix-assisted laser desorption/ionization mass spectrometry (WO 99/57318), and combinations of such methods.
In some cases, genomic DNA can be used to detect the T allele of rs2519093. Genomic DNA typically is extracted from a biological sample such as a peripheral blood sample, but can be extracted from other biological samples, including tissues (e.g., mucosal scrapings of the lining of the mouth or from renal or hepatic tissue). Any appropriate method can be used to extract genomic DNA from a blood or tissue sample, including, for example, phenol extraction. In some cases, genomic DNA can be extracted with kits such as the QIAamp® Tissue Kit (Qiagen, Chatsworth, Calif.), the Wizard® Genomic DNA purification kit (Promega, Madison, Wis.), the Puregene DNA Isolation System (Gentra Systems, Minneapolis, Minn.), or the A.S.A.P.3 Genomic DNA isolation kit (Boehringer Mannheim, Indianapolis, Ind.).
An amplification step can be performed before proceeding with the detection method. For example, ABO nucleic acid can be amplified and then directly sequenced. Dye primer sequencing can be used to increase the accuracy of detecting heterozygous samples.
As described herein, the presence of the T allele of rs2519093 in a mammal (e.g., human) can indicate that that mammal has an increased susceptibility of developing venous thromboembolism. In some cases, the presence of the T allele of rs2519093 in a human in combination with the presence of a G allele of rs6025, a G allele of rs1799963, and/or a mutant allele of rs8176719 can indicate that that human has an increased susceptibility of developing venous thromboembolism. In some cases, the presence of the T allele of rs2519093 in a human can indicate that that human has an increased susceptibility of developing venous thromboembolism, especially when that human also includes a family history of inherited thrombophilia and/or venous thromboembolism. For example, the presence of the T allele of rs2519093 in a human in combination with a family history of the Factor V Leiden (G allele of rs6025) and/or prothrombin G20210A (G allele of rs1799963) mutations can indicate that that human has an increased susceptibility of developing venous thromboembolism.
In some cases, any human containing one or two T alleles of rs2519093 can be classified as having an elevated risk of developing venous thromboembolism. For example, a human having one or two T alleles of rs2519093 can be classified as having an elevated risk of developing venous thromboembolism when the human is any age (e.g., less than 65, 60, 55, 50, 45, 40, or 35 years old), does or does not appear to have a family history of venous thromboembolism, or has or has not had a positive or negative diagnostic test for venous thromboembolism. In some cases, a human having one or two T alleles of rs2519093 can be classified as having an elevated risk of developing venous thromboembolism when the human also has a G allele of rs6025, a G allele of rs1799963, and/or a mutant allele of rs8176719.
This document also provides methods and materials related to preventing a human identified as being susceptible to develop venous thromboembolism as described herein from developing venous thromboembolism. For example, a human can be identified as being likely to develop venous thromboembolism if it is determined that the mammal has the T allele of rs2519093. After identifying a human as being likely to develop venous thromboembolism, a health-care professional can take one or more actions that can affect the mammal's care. For example, a health-care professional can record information regarding the presence of the T allele of rs2519093, the presence of one T allele of rs2519093, or the presence of two T alleles of rs2519093 in the human's medical record. In some cases, a health-care professional can record a diagnosis of being likely to develop venous thromboembolism, or otherwise transform the human's medical record, to reflect that the human is susceptible to developing venous thromboembolism. In some cases, a health-care professional can review and evaluate the human's medical record, and can assess multiple preventative treatment strategies for clinical intervention of the human's susceptibility to develop venous thromboembolism. In some cases, a health-care professional can instruct the human to (a) perform active movements (e.g., move their legs often or take a walk during long plane trips, car trips, and other situations in which they are sitting or lying down for long periods of time), (b) undergo heparin prophylaxis (e.g., low doses of heparin injected under the skin), and/or (c) wear clothes items that provide intermittent pneumatic compression (e.g., soft boots that automatically and gently squeeze the calves periodically).
In some cases, one or more of the genetic variations (e.g., SNPs or single nucleotide variants (SNVs)) provided herein (e.g., provided in Table 4 or Table 12) can be used in place of or in combination with rs2519093 to perform a method provided herein. For example, a human containing one or two T alleles of rs495828 can be classified as having an elevated risk of developing venous thromboembolism. For example, a human having one or two T alleles of rs495828 can be classified as having an elevated risk of developing venous thromboembolism when the human is any age (e.g., less than 65, 60, 55, 50, 45, 40, or 35 years old), does or does not appear to have a family history of venous thromboembolism, or has or has not had a positive or negative diagnostic test for venous thromboembolism. In some cases, as described herein, after identifying a human as being likely to develop venous thromboembolism, a health-care professional can take one or more actions that can affect the mammal's care. For example, a health-care professional can record information regarding the presence of the T allele of rs495828, the presence of one T allele of rs495828, or the presence of two T alleles of rs495828 in the human's medical record. In some cases, a health-care professional can record a diagnosis of being likely to develop venous thromboembolism, or otherwise transform the human's medical record, to reflect that the human is susceptible to developing venous thromboembolism. In some cases, a health-care professional can review and evaluate the human's medical record, and can assess multiple preventative treatment strategies for clinical intervention of the human's susceptibility to develop venous thromboembolism. In some cases, a health-care professional can instruct the human to (a) perform active movements (e.g., move their legs often or take a walk during long plane trips, car trips, and other situations in which they are sitting or lying down for long periods of time), (b) undergo heparin prophylaxis (e.g., low doses of heparin injected under the skin), and/or (c) wear clothes items that provide intermittent pneumatic compression (e.g., soft boots that automatically and gently squeeze the calves periodically).
The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.
EXAMPLES Example 1 The rs2519093 SNP Can Identify Patients with an Increased Susceptibility to Venous Thromboembolism A clinic-based case-control study was performed to test genetic variation within genes from the anticoagulant, procoagulant, fibrinolytic, and innate immunity pathways for an association with venous thromboembolism (VTE).
The cases were obtained from Mayo Clinic Caucasian outpatient adults with objectively-diagnosed deep vein thrombosis (DVT) or pulmonary embolism (PE) without active cancer or mechanical thrombosis. Controls were obtained from Mayo Clinic outpatients without VTE, and were frequency-matched on case age group, sex, and race. The primary outcome was VTE status (yes/no) with covariates age at blood draw, sex, stroke, and/or myocardial infarction status, and state of residence (FIG. 1).
To annotate the anticoagulant, procoagulant, fibrinolytic, and innate immunity pathways, 749 candidate genes were selected from three electronic databases: Kyoto Encyclopedia of Genes and Genomes (Complement & Coagulation Cascades); NHLBI Program for Genomic Applications (Fibrinolytic); Univ. of Washington FHCRC Variation Discovery Resource (Innate Immunity).
SNPs were selected 10 kb upstream and downstream of each gene using HapMap (http://www.hapmap.org), Perlegen (http://www/perlegen.com), Seattle SNPs (http://pga.mbt.washington.edu/), and NIEHS SNPs (http://egp.gs.washington.edu/) using r2 of 0.8 and a minor allele frequency ≧0.005 (FIG. 2).
13,027 SNPs were genotyped using Illumina Infinium iSelect platform, and four SNPs (three ABO blood type and prothrombin G20210A) using TaqMan.
261 individuals were excluded due to inclusion criteria, genotype issues, call rate <0.95, being non-Caucasian, and relatedness. After cleaning, 12,313 SNPs were used. Multidimensional scaling was used for population stratification with 500 ancestry informative markers (FIG. 3).
Unconditional logistic regression was performed to test for association between each SNP and VTE status adjusted for age, sex, stroke/MI status, and state of residence. Results using an additive genetic model are shown in FIGS. 4-9. Individual and joint population attributable risks for the risk genotypes for F5 mutation (rs6025), F2 G20210A mutation (rs1799963), the ABO blood type O SNP (rs8176719), and an ABO SNP (rs2519093) are presented in FIG. 7. All analyses were performed using PLINK v 1.05.
These results demonstrate that the presence of the rs2519093 ABO SNP, either alone or in combination with the rs6025 Factor V SNP, the rs1799963 prothrombin SNP, and/or the rs8176719 ABO blood type O SNP, can indicate that a particular person is susceptible to develop VTE. These results also demonstrate that the rs1799963 prothrombin SNP, the rs2519093 ABO SNP, and the rs8176719 ABO blood type O SNP can indicate susceptibility to develop VTE independent of Factor V Leiden status (e.g., rs6025).
Example 2 Genetic Variation Within the Anticoagulant, Procoagulant, Fibrinolytic, and Innate Immunity Pathways as Risk Factors for Venous Thromboembolism The following was performed as part of the work described in Example 1.
Study Setting and Population Consecutive Mayo Clinic outpatients age 18 years or older with objectively-diagnosed deep vein thrombosis (DVT) or pulmonary embolism (PE) who resided in the upper Midwest United States and who were referred to the Mayo Clinic Special Coagulation Laboratory or Thrombophilia Center over the study period were approached for study participation. Patients with VTE related to active cancer, an indwelling central venous catheter, transvenous pacemaker or other mechanical cause for thrombosis, a lupus anticoagulant or other antiphospholipid antibodies, vasculitis or a vascular anomaly (e.g., Klippel-Trenaunay), other autoimmune disorders (including heparin-induced thrombocytopenia) or prior bone marrow or liver transplantation were excluded. A DVT or PE was categorized as objectively diagnosed when confirmed by venography, pulmonary angiography, compression venous duplex ultrasonography, ventilation/perfusion lung scan interpreted as high probability for PE, computed tomographic pulmonary angiography, magnetic resonance imaging or pathology examination of thrombus removed at surgery. Clinic-based controls were prospectively selected from persons undergoing outpatient general medical examinations within the Mayo Clinic Divisions of General Internal Medicine and Primary Care Internal Medicine, Department of Internal Medicine, general internal medicine practices that care for patients (>10,000 per year) from the upper Midwest United States. Additional controls were recruited from the Department of Family Medicine and the Mayo Clinic Sports Medicine Center. Controls were frequency matched on the age group (20-29, 30-39, 40-49, 50-59, 60-69, 70-79 years), sex, state of residence and myocardial infarction (MI)/stroke status distribution of the cases, and had no previous diagnosis of VTE or superficial vein thrombosis. Potential controls with active cancer, antiphospholipid antibody syndrome, rheumatologic or other autoimmune disorder, or prior bone marrow or liver transplant were excluded.
For consenting cases and controls, data were collected by in-person questionnaire and medical record review on prior history of VTE and date(s) of VTE (for cases), other thrombotic events and dates of thrombosis (e.g., stroke, MI, peripheral artery thrombosis), current medications and prior exposures (and dates of exposures) that are VTE risk factors, including surgery, hospitalization for acute medical illness, trauma/fracture and neurological disease with leg paresis, and for women, oral contraceptives, obstetric history, and hormone therapy. Cases and controls provided informed consent to use of a venous whole blood sample for leukocyte genomic DNA extraction, storage and use for research addressing the genetics of VTE. The study was approved by the Mayo Clinic Institutional Review Board.
Candidate Gene Selection Candidate genes were selected from three electronic databases (i.e., Kyoto Encyclopedia of Genes and Genomes [Complement & Coagulation Cascades]; NHLBI Program for Genomic Applications; Univ. of Washington FHCRC Variation Discovery Resource [Innate Immunity]) that annotate anticoagulant, procoagulant, fibrinolytic, and/or innate immunity pathways. In general, the focus was on platelet, monocyte, neutrophil and endothelial cell agonists, receptors, ligands, signal transduction and adhesion molecules, granule contents and effectors; plasma proteases (procoagulant, anticoagulant, fibrinolytic and complement [including cofactors and receptors]) and inhibitors (e.g., serine protease inhibitors); matrix metalloproteases; inflammatory cytokines and receptors (including leukotrienes and receptors); estrogen, progesterone and androgen receptors, co-regulators and enzymes related to estrogen metabolism; important enzymes for catechol, homocysteine, thromboxane A2 and prostacyclin biosynthesis and metabolism; and 3-Hydroxy-3-Methylglutaryl Coenzyme A (HMG-CoA) reductase.
SNP Identification and Selection To identify SNPs for the custom 16,720 bead Illumina Infinium (14,612 SNPs) genotyping panel, genotypes from the genome-wide genotyping projects HapMap (http://www.hapmap.org) and Perlegen (http://www.perlegen.com) were used. Additionally, genotypes from two gene resequencing programs were used: Seattle SNPs (http://pga.mbt.washington.edu/) and NIEHS SNPs (http://egp.gs.washington.edu/). To determine the HapMap and Perlegen SNPs for each of the 764 candidate genes, SNPs 10kb upstream and downstream of each gene were picked. The gene and SNP coordinates were based on NCBI build 35 and dbSNP build 125. If the gene had been resequenced in Seattle SNPs or NIEHS SNPs, genotypes from those sources were used as well. At the time the SNP selection, Seattle SNPs had resequenced 205 of the candidate genes and NIEHS SNPs had resequenced 20.
A hierarchical approach was used for SNP selection. To select Id tagSNPs, IdSelect (Carlson et al., American Journal of Human Genetics., 74:106-20 (2004)) was run on each candidate gene for the Caucasian samples within each public genotype source (HapMap, Perlegen, Seattle, NIEHS). An r2 of 0.8 and a minor allele frequency (MAF) cutoff of 0.05 were used with the exception of one gene (GP9-Entrez gene id 2815) where a MAF cutoff of 0.01 was used. To determine the best source of genotypes for each gene where a gene had been resequenced, the source with the higher number of Id bins for the Caucasian samples after removing bins with no tag SNP meeting the minimum Illumina design score (design score=0.4) was used. If each source (e.g., HapMap, Seattle SNPs) had the same number of bins, HapMap was used as the best source because of its higher number of samples (60 unrelated Caucasian samples). HapMap was chosen as the best source for 626 genes, Seattle for 88 genes, Perlegen for 26 genes and NIEHS for 6 genes. Eighteen genes had no tagSNPs because no SNPs had a MAF≧0.05 or met the minimum acceptable Illumina design score or wasn't mapped to the genome reference assembly. If possible, additional tag SNPs were selected when the bin was large. If there were ≧30 or ≧10 SNPs in an Id bin, three and two tag SNPs per bin, respectively, were chose. After completing this process, 12,577 Id tagSNPs, representing 12073 Id bins, were selected for genotyping. 485 bins were dropped due to low design scores.
Nonsynonymous coding (nc)SNPs with a MAF ≧0.005, which met the minimum acceptable Illumina design score, were next selected. For Perlegen and HapMap ncSNPs, the MAF was used for Caucasian samples. For ncSNPs not in those sources, the MAF for Caucasian samples in the Illumina annotation were used. This added 675 ncSNPs to the panel. Next, eight SNPs were added that had been identified in the literature and with collaborators. To test for population stratification, 557 ancestry informative markers were included (Seldin et al., PLoS Genetics., 2:e143 (2006)). Finally, to fill out the panel, 795 additional SNPs were added from the genes and with MAF ≧5%, resulting in a total of 14,612 SNPs. A list of the candidate genes and number of selected SNPs for each gene is provided in Table 1.
TABLE 1
Number Number of
Gene of Manufactured SNPs passed Number of
Name Gene ID Description Chromosome Gene Location Gene Start Gene Stop SNPs the Quality Control Analyzed SNPs
A2M 2 alpha-2-macroglobulin 12 12p13.31 9111571 9159825 11 10 10
ABCF1 23 ATP-binding cassette, sub-family F 6 6p21.33 30647149 30667288 3 3 3
(GCN20), member 1
ABO 28 ABO blood group (transferase A, alpha 1- 9 9q34.2 135120384 135140451 20 17 17
3-N-acetylgalactosaminyltransferase;
transferase B, alpha 1-3-
galactosyltransferase)
ACE 1636 angiotensin I converting enzyme 17 17q23.3 58908166 58928711 7 7 6
(peptidyl-dipeptidase A) 1
ACE2 59272 angiotensin I converting enzyme X Xp22 15489077 15529058 6 5 5
(peptidyl-dipeptidase A) 2
ACHE 43 acetylcholinesterase (Yt blood group) 7 7q22 100325551 100331477 7 6 6
ACVR1 90 activin A receptor, type I 2 2q23-q24 158301207 158403036 15 15 15
ACVR2A 92 activin A receptor, type IIA 2 2q22.3 148319040 148404863 8 8 8
ACVR2B 93 activin A receptor, type IIB 3 3p22 38470794 38509637 4 4 4
ADAM17 6868 ADAM metallopeptidase domain 17 2 2p25 9546843 9613368 9 9 9
(tumor necrosis factor, alpha, converting
enzyme)
ADAMTS13 11093 ADAM metallopeptidase with 9 9q34 135276941 135314328 8 7 7
thrombospondin type 1 motif, 13
ADORA1 134 adenosine A1 receptor 1 1q32.1 201363459 201403156 20 19 19
ADORA2A 135 adenosine A2a receptor 22 22q11.23 23153530 23168325 4 3 3
ADRB2 154 adrenergic, beta-2-, receptor, surface 5 5q31-q32 148186349 148188381 12 11 11
AGT 183 angiotensinogen (serpin peptidase 1 1q42-q43 228904892 228916564 20 20 20
inhibitor, clade A, member 8)
AGTR1 185 angiotensin II receptor, type 1 3 3q24 149898348 149943480 17 17 17
AGTR2 186 angiotensin II receptor, type 2 X Xq22-q23 115215986 115220253 5 5 5
AHSG 197 alpha-2-HS-glycoprotein 3 3q27 187813544 187821801 13 13 13
AIF1 199 allograft inflammatory factor 1 6 6p21.3 31691012 31692777 3 3 3
AKT2 208 v-akt murine thymoma viral oncogene 19 19q13.1-q13.2 45428064 45483105 2 2 2
homolog 2
ALOX12 239 arachidonate 12-lipoxygenase 17 17p13.1 6840108 6854779 14 13 13
ALOX15 246 arachidonate 15-lipoxygenase 17 17p13.3 4480963 4491709 12 11 11
ALOX5 240 arachidonate 5-lipoxygenase 10 10q11.2 45189635 45261571 16 16 16
ALOX5AP 241 arachidonate 5-lipoxygenase-activating 13 13q12 30207669 30236556 28 26 26
protein
AMH 268 anti-Mullerian hormone 19 19p13.3 2200113 2203072 7 6 6
AMHR2 269 anti-Mullerian hormone receptor, type II 12 12q13 52103908 52111579 3 3 3
ANKRD30B 374860 ankyrin repeat domain 30B 18 18p11.21 14738239 14844028 8 5 5
ANXA1 301 annexin A1 9 9q12-q21.2| 74956601 74975127 15 15 15
9q12-q21.2
ANXA2 302 annexin A2 15 15q22.2 58426642 58477477 52 49 49
ANXA3 306 annexin A3 4 4q13-q22 79691766 79750629 13 12 12
ANXA5 308 annexin A5 4 4q26-q28|4q27 122808598 122837626 11 11 11
APCS 325 amyloid P component, serum 1 1q21-q23 157824240 157825285 10 10 10
APOA2 336 apolipoprotein A-II 1 1q21-q23 159458707 159460042 14 14 14
APOH 350 apolipoprotein H (beta-2-glycoprotein I) 17 17q23-qter 61638609 61656018 20 19 19
APOL2 23780 apolipoprotein L, 2 22 22q12 34952201 34965946 19 19 19
APOL3 80833 apolipoprotein L, 3 22 22q13.1 34866323 34892171 25 23 23
APP 351 amyloid beta (A4) precursor protein 21 21q21.2|21q21.3 26174732 26465003 52 51 51
(peptidase nexin-II, Alzheimer disease)
AR 367 androgen receptor (dihydrotestosterone X Xq12 66680599 66860844 6 6 6
receptor; testicular feminization; spinal
and bulbar muscular atrophy; Kennedy
disease)
ARHGEF1 9138 Rho guanine nucleotide exchange factor 19 19q13.13 47079107 47103444 2 2 2
(GEF) 1
ARRB1 408 arrestin, beta 1 11 11q13 74654130 74740521 15 15 15
ART4 420 ADP-ribosyltransferase 4 (Dombrock 12 12p13-p12 14873512 14887680 14 13 13
blood group)
ASB1 51665 ankyrin repeat and SOCS box-containing 1 2 2q37 239000365 239025630 6 6 6
ATF2 1386 activating transcription factor 2 2 2q32 175647252 175741143 12 11 11
ATF4 468 activating transcription factor 4 (tax- 22 22q13.1 38246515 38248637 5 4 4
responsive enhancer element B67)
ATRN 8455 attractin 20 20p13 3399676 3579765 42 42 42
AZU1 566 azurocidin 1 (cationic antimicrobial 19 19p13.3 778831 783017 7 7 7
protein 37)
BAG4 9530 BCL2-associated athanogene 4 8 8p11.23 38153263 38187694 4 4 4
BATF 10538 basic leucine zipper transcription factor, 14 14q24.3 75058537 75083086 10 9 9
ATF-like
BCAM 4059 basal cell adhesion molecule (Lutheran 19 19q13.2 50004178 50016518 10 10 10
blood group)
BCL2 596 B-cell CLL/lymphoma 2 18 18q21.33|18q21.3 58941559 59137593 62 60 60
BCL2A1 597 BCL2-related protein A1 15 15q24.3 78040290 78050698 9 9 9
BCL3 602 B-cell CLL/lymphoma 3 19 19q13.1-q13.2 49943820 49955141 4 4 4
BCL5 603 B-cell CLL/lymphoma 5 17 17q23.2 0 0 0
BCL6 604 B-cell CLL/lymphoma 6 (zinc finger 3 3q27 188921859 188946169 12 12 12
protein 51)
BCO2 83875 beta-carotene oxygenase 2 11 11q22.3-q23.1 111551418 111594862 12 12 12
BDKRB1 623 bradykinin receptor B1 14 14q32.1-q32.2 95792312 95800853 12 12 12
BDKRB2 624 bradykinin receptor B2 14 14q32.1-q32.2 95740950 95780542 30 29 29
BHMT 635 betaine-homocysteine methyltransferase 5 5q13.1-q15 78443360 78463869 10 10 10
BIRC3 330 baculoviral IAP repeat-containing 3 11 11q22 101693404 101713675 2 2 2
BLNK 29760 B-cell linker 10 10q23.2-q23.33 97941445 98021316 34 33 33
BMPR1A 657 bone morphogenetic protein receptor, 10 10q22.3 88506376 88674925 16 15 15
type IA
BMPR1B 658 bone morphogenetic protein receptor, 4 4q22-q24 95898151 96295099 40 39 39
type IB
BMPR2 659 bone morphogenetic protein receptor, 2 2q33-q34 202949916 203140719 12 10 10
type II (serine/threonine kinase)
BPI 671 bactericidal/permeability-increasing 20 20q11.23 36365966 36399319 31 30 30
protein
C1QA 712 complement component 1, q 1 1p36.12 22835705 22838762 9 7 7
subcomponent, A chain
C1QB 713 complement component 1, q 1 1p36.12 22852269 22860616 15 14 14
subcomponent, B chain
C1QBP 708 complement component 1, q 17 17p13.3 5276823 5283195 5 4 4
subcomponent binding protein
C1QC 714 complement component 1, q 1 1p36.11 22842734 22847190 12 10 10
subcomponent, C chain
C1QL1 10882 complement component 1, q 17 17q21 40392587 40401170 11 11 11
subcomponent-like 1
C1QL3 389941 complement component 1, q 10 10p13 16595748 16604010 9 9 9
subcomponent-like 3
C1R 715 complement component 1, r 12 12p13 11 11 11
subcomponent
C1S 716 complement component 1, s 12 12p13 7038278 7048597 7 6 6
subcomponent
C2 717 complement component 2 6 6p21.3 32003473 32021427 18 18 18
C3 718 complement component 3 19 19p13.3-p13.2 6628846 6671662 36 30 30
C3AR1 719 complement component 3a receptor 1 12 12p13.31 8102186 8110222 4 3 3
C4A 720 complement component 4A (Rodgers 6 6p21.3 32090549 32111173 4 1 1
blood group)
C4BPA 722 complement component 4 binding 1 1q32 205344230 205384940 18 17 17
protein, alpha
C4BPB 725 complement component 4 binding 1 1q32 205328835 205339961 8 8 8
protein, beta
C5 727 complement component 5 9 9q33-q34 122754434 122852375 24 23 23
C5AR1 728 complement component 5a receptor 1 19 19q13.3-q13.4 52504944 52517167 1 0 0
C6 729 complement component 6 5 5p13 41178093 41249369 20 19 19
C7 730 complement component 7 5 5p13 40945356 41018798 27 25 25
C8A 731 complement component 8, alpha 1 1p32 57093065 57156482 17 16 16
polypeptide
C9 735 complement component 9 5 5p14-p12 39320758 39400412 14 14 14
CADM1 23705 cell adhesion molecule 1 11 11q23.2 114549555 114880451 59 58 57
CAMK1D 57118 calcium/calmodulin-dependent protein 10 10p13 12431589 12911741 199 192 191
kinase ID
CAPRIN2 65981 caprin family member 2 12 12p11 30753753 30798715 12 12 12
CARM1 10498 coactivator-associated arginine 19 19p13.2 10843253 10894448 7 7 7
methyltransferase 1
CASP1 834 caspase 1, apoptosis-related cysteine 11 11q23 104401445 104411067 9 8 8
peptidase (interleukin 1, beta, convertase)
CASP10 843 caspase 10, apoptosis-related cysteine 2 2q33-q34 201755866 201802355 6 6 6
peptidase
CASP4 837 caspase 4, apoptosis-related cysteine 11 11q22.2-q22.3 104318804 104344535 9 9 9
peptidase
CAV1 857 caveolin 1, caveolae protein, 22 kDa 7 7q31.1 115952075 115988466 14 14 14
CBS 875 cystathionine-beta-synthase 21 21q22.3 43346370 43369490 25 22 22
CCL1 6346 chemokine (C-C motif) ligand 1 17 17q12 29711512 29714365 5 5 5
CCL11 6356 chemokine (C-C motif) ligand 11 17 17q21.1-q21.2 29636800 29639312 11 11 11
CCL13 6357 chemokine (C-C motif) ligand 13 17 17q11.2 29707584 29709742 7 6 6
CCL15 6359 chemokine (C-C motif) ligand 15 17 17q11.2 31348777 31353125 10 9 9
CCL16 6360 chemokine (C-C motif) ligand 16 17 17q11.2 31327648 31332636 5 5 5
CCL17 6361 chemokine (C-C motif) ligand 17 16 16q13 55996180 56007475 8 8 8
CCL18 6362 chemokine (C-C motif) ligand 18 17 17q11.2 31415756 31422954 5 5 5
(pulmonary and activation-regulated)
CCL19 6363 chemokine (C-C motif) ligand 19 9 9p13 34679567 34681274 5 5 5
CCL2 6347 chemokine (C-C motif) ligand 2 17 17q11.2-q12 29606409 29608335 7 7 7
CCL20 6364 chemokine (C-C motif) ligand 20 2 2q33-q37 228386814 228390494 8 7 7
CCL21 6366 chemokine (C-C motif) ligand 21 9 9p13 34699002 34700147 4 4 4
CCL22 6367 chemokine (C-C motif) ligand 22 16 16q13 55950219 55957602 9 9 9
CCL23 6368 chemokine (C-C motif) ligand 23 17 17q12 31364210 31369118 6 5 5
CCL24 6369 chemokine (C-C motif) ligand 24 7 7q11.23 75279050 75280969 11 11 11
CCL25 6370 chemokine (C-C motif) ligand 25 19 19p13.2 8023934 8033547 15 15 15
CCL26 10344 chemokine (C-C motif) ligand 26 7 7q11.23 75236778 75257000 3 2 2
CCL3 6348 chemokine (C-C motif) ligand 3 17 17q12 31439715 31441619 8 7 7
CCL3L1 6349 chemokine (C-C motif) ligand 3-like 1 17 17q21.1 31647955 31649843 0 0 0
CCL4 6351 chemokine (C-C motif) ligand 4 17 17q12 31455333 31457127 8 6 6
CCL4L1 9560 chemokine (C-C motif) ligand 4-like 1 17 17q12 31562581 31564388 0 0 0
CCL5 6352 chemokine (C-C motif) ligand 5 17 17q11.2-q12 31222608 31231490 3 3 3
CCL7 6354 chemokine (C-C motif) ligand 7 17 17q11.2-q12 29621353 29623369 11 10 10
CCL8 6355 chemokine (C-C motif) ligand 8 17 17q11.2 29670179 29672534 13 12 12
CCR1 1230 chemokine (C-C motif) receptor 1 3 3p21 46218204 46224836 6 6 6
CCR10 2826 chemokine (C-C motif) receptor 10 17 17q21.1-q21.3 38084946 38087371 3 3 3
CCR2 1231 chemokine (C-C motif) receptor 2 3|NT_113884.1 42313 49515 2 2 2
CCR3 1232 chemokine (C-C motif) receptor 3 3 3p21.3 46258692 46283166 14 14 14
CCR4 1233 chemokine (C-C motif) receptor 4 3 3p24 32968070 32971407 3 3 3
CCR5 1234 chemokine (C-C motif) receptor 5 3 3p21.31 46386637 46392701 2 2 2
CCR6 1235 chemokine (C-C motif) receptor 6 6 6q27 167445285 167472619 20 20 20
CCR7 1236 chemokine (C-C motif) receptor 7 17 17q12-q21.2 35963547 35975250 5 5 5
CCR8 1237 chemokine (C-C motif) receptor 8 3 3p22 39346219 39351077 4 4 4
CCR9 10803 chemokine (C-C motif) receptor 9 3 3p21.3 45903023 45919671 12 12 11
CCRL1 51554 chemokine (C-C motif) receptor-like 1 3 3q22 133798784 133804072 2 2 2
CCRL2 9034 chemokine (C-C motif) receptor-like 2 3 3p21 46423725 46426018 0 0 0
CD14 929 CD14 molecule 5 5q22-q32| 139991501 139993439 5 4 4
5q31.1
CD180 4064 CD180 molecule 5 5q12 66513872 66528368 15 15 15
CD1B 910 CD1b molecule 1 1q22-q23 156564364 156567945 5 5 5
CD1C 911 CD1c molecule 1 1q22-q23 156526187 156531188 2 2 2
CD1D 912 CD1d molecule 1 1q22-q23 156416361 156422841 9 9 9
CD22 933 CD22 molecule 19 19q13.1 40511919 40530104 17 17 17
CD27 939 CD27 molecule 12 12p13 6424312 6431145 23 23 23
CD276 80381 CD276 molecule 15 15q23-q24 71763675 71793912 8 8 8
CD28 940 CD28 molecule 2 2q33 204279443 204310801 9 8 8
CD36 948 CD36 molecule (thrombospondin 7 7q11.2 80069459 80144262 11 10 10
receptor)
CD4 920 CD4 molecule 12 12pter-p12 6768912 6800237 17 16 16
CD40 958 CD40 molecule, TNF receptor 20 20q12-q13.2 44180313 44191791 12 12 12
superfamily member 5
CD40LG 959 CD40 ligand (TNF superfamily, member X Xq26 135558002 135570215 4 4 4
5, hyper-IgM syndrome)
CD44 960 CD44 molecule (Indian blood group) 11 11p13 35116993 35210525 53 52 52
CD46 4179 CD46 molecule, complement regulatory 1 1q32 205992025 206035481 45 40
protein
CD47 961 CD47 molecule 3 3q13.1-q13.2 109244631 109292625 6 6 6
CD53 963 CD53 molecule 1 1p13 111215344 111244081 14 13 13
CD55 1604 CD55 molecule, decay accelerating factor 1 1q32 205561488 205600470 49 46 46
for complement (Cromer blood group)
CD58 965 CD58 molecule 1 1p13 116858680 116915126 7 6 6
CD59 966 CD59 molecule, complement regulatory 11 11p13 33681132 33714600 49 46 46
protein
CD74 972 CD74 molecule, major histocompatibility 5 5q32 149761393 149772525 12 12 12
complex, class II invariant chain
CD80 941 CD80 molecule 3 3q13.3-q21 120725830 120761171 26 26 26
CD83 9308 CD83 molecule 6 6p23 14225844 14245128 18 18 18
CD86 942 CD86 molecule 3 3q21 123256911 123322673 23 21 21
CD9 928 CD9 molecule 12 12p13.3 6179816 6217688 9 9 9
CD97 976 CD97 molecule 19 19p13 14353213 14380535 14 11 11
CDH5 1003 cadherin 5, type 2, VE-cadherin (vascular 16 16q22.1 64958064 64996190 19 19 19
epithelium)
CEBPB 1051 CCAAT/enhancer binding protein 20 20q13.1 48240783 48242619 3 3 3
(C/EBP), beta
CEBPD 1052 CCAAT/enhancer binding protein 8 8p11.2-p11.1 48812029 48813279 0 0 0
(C/EBP), delta
CFB 629 complement factor B 6 6p21.3 32021752 32027839 19 19 19
CFD 1675 complement factor D (adipsin) 19 19p13.3 810665 814624 7 7 7
CFH 3075 complement factor H 1 1q32 194887764 194983257 32 14 14
CFHR1 3078 complement factor H-related 1 1 1q32 195055484 195067942 5 1 1
CFI 3426 complement factor I 4 4q25 110881297 110942783 8 8 8
CFLAR 8837 CASP8 and FADD-like apoptosis 2 2q33-q34 201689135 201737260 2 2 2
regulator
CFP 5199 complement factor properdin X Xp11.4 47368569 47374648 6 5 5
CHST1 8534 carbohydrate (keratan sulfate Gal-6) 11 11p11.2 45627003 45643748 7 7 7
sulfotransferase 1
CHUK 1147 conserved helix-loop-helix ubiquitous 10 10q24-q25 101938114 101979334 8 8 8
kinase
CISH 1154 cytokine inducible SH2-containing 3 3p21.3 50618924 50624207 0 0 0
protein
CITED2 10370 Cbp/p300-interacting transactivator, with 6 6q23.3 139735089 139737478 3 3 3
Glu/Asp-rich carboxy-terminal domain, 2
CKLF 51192 chemokine-like factor 16 16q21 65143967 65157655 5 5 5
CLC 1178 Charcot-Leyden crystal protein 19 19q13.1 44913735 44920508 10 9 9
CLEC4E 26253 C-type lectin domain family 4, member E 12 12p13.31 8577168 8584825 9 9 9
CNTFR 1271 ciliary neurotrophic factor receptor 9 9p13 34541431 34579722 18 17 17
COL18A1 80781 collagen, type XVIII, alpha 1 21 21q22.3 45649525 45758062 31 28 28
COL1A1 1277 collagen, type I, alpha 1 17 17q21.33 45616456 45633999 11 10 10
COL1A2 1278 collagen, type I, alpha 2 7 7q22.1 93861809 93898480 32 29 29
COL4A1 1282 collagen, type IV, alpha 1 13 13q34 109599311 109757497 77 74 74
COLEC10 10584 collectin sub-family member 10 (C-type 8 8q23-q24.1 120148627 120188388 15 15 15
lectin)
COLEC12 81035 collectin sub-family member 12 18 18pter-p11.3 309356 490685 106 103 103
CP1 50820 Cleft palate, isolated 2 2q33 0 0 0
CPB2 1361 carboxypeptidase B2 (plasma) 13 13q14.11 45525323 45577212 108 92 92
CR1 1378 complement component (3b/4b) receptor 1 1q32 205736096 205881733 28 26 26
1 (Knops blood group)
CR2 1380 complement component (3d/Epstein Barr 1 1q32 205694293 205729863 26 25 25
virus) receptor 2
CRADD 8738 CASP2 and RIPK1 domain containing 12 12q21.33-q23.1 92595282 92768663 48 48 48
adaptor with death domain
CREB1 1385 cAMP responsive element binding 2 2q34 208102931 208171818 6 6 6
protein 1
CREBBP 1387 CREB binding protein (Rubinstein-Taybi 16 16p13.3 3715056 3870122 11 10 10
syndrome)
CREM 1390 cAMP responsive element modulator 10 10p11.21 35455807 35541892 6 6 6
CRLF1 9244 cytokine receptor-like factor 1 19 19p12 18565047 18578660 6 5 5
CRLF2 64109 cytokine receptor-like factor 2 X|Y Xp22.3; 0 0 0
Yp11.3
CRP 1401 C-reactive protein, pentraxin-related 1 1q21-q23 157948703 157951003 17 17 17
CSF1R 1436 colony stimulating factor 1 receptor, 5 5q32 149413051 149473128 29 28 28
formerly McDonough feline sarcoma
viral (v-fms) oncogene homolog
CSF2 1437 colony stimulating factor 2 (granulocyte- 5 5q31.1 131437384 131439758 10 9 9
macrophage)
CSF2RA 1438 colony stimulating factor 2 receptor, X|Y Xp22.32 and 0 0 0
alpha, low-affinity (granulocyte- Yp11.3
macrophage)
CSF2RB 1439 colony stimulating factor 2 receptor, beta, 22 22q13.1 35648168 35664764 17 17 17
low-affinity (granulocyte-macrophage)
CSF3 1440 colony stimulating factor 3 (granulocyte) 17 17q11.2-q12 35425214 35427592 6 6 6
CSF3R 1441 colony stimulating factor 3 receptor 1 1p35-p34.3 36704231 36721096 12 11 11
(granulocyte)
CX3CL1 6376 chemokine (C—X3—C motif) ligand 1 16 16q13 55963915 55976457 9 9 9
CX3CR1 1524 chemokine (C—X3—C motif) receptor 1 3 3p21|3p21.3 39279989 39296531 17 16 16
CXCL1 2919 chemokine (C—X—C motif) ligand 1 4 4q21 74953973 74955817 7 7 7
(melanoma growth stimulating activity,
alpha)
CXCL10 3627 chemokine (C—X—C motif) ligand 10 4 4q21 77161295 77163674 11 9 9
CXCL11 6373 chemokine (C—X—C motif) ligand 11 4 4q21.2 77173859 77176257 7 6 6
CXCL12 6387 chemokine (C—X—C motif) ligand 12 10 10q11.1 44185611 44200548 19 19 19
(stromal cell-derived factor 1)
CXCL13 10563 chemokine (C—X—C motif) ligand 13 (B- 4 4q21 78651931 78752010 5 5 5
cell chemoattractant)
CXCL14 9547 chemokine (C—X—C motif) ligand 14 5 5q31 134934274 134942868 11 11 11
CXCL16 58191 chemokine (C—X—C motif) ligand 16 17 17p13 4583577 4589972 12 12 12
CXCL2 2920 chemokine (C—X—C motif) ligand 2 4 4q21 75181616 75183861 1 1 1
CXCL3 2921 chemokine (C—X—C motif) ligand 3 4 4q21 75121170 75123354 2 2 2
CXCL5 6374 chemokine (C—X—C motif) ligand 5 4 4q13.3 75080223 75083280 7 4 4
CXCL6 6372 chemokine (C—X—C motif) ligand 6 4 4q21 74921277 74923341 4 4 4
(granulocyte chemotactic protein 2)
CXCL9 4283 chemokine (C—X—C motif) ligand 9 4 4q21 77141647 77147665 8 7 7
CXCR3 2833 chemokine (C—X—C motif) receptor 3 X Xq13 70752491 70755092 2 2 2
CXCR4 7852 chemokine (C—X—C motif) receptor 4 2 2q21 136588389 136592195 6 6 6
CXCR5 643 chemokine (C—X—C motif) receptor 5 11 11q23.3 118259777 118272181 10 9 9
CXCR6 10663 chemokine (C—X—C motif) receptor 6 3 3p21 45959977 45964849 8 6 6
CYBB 1536 cytochrome b-245, beta polypeptide X Xp21.1 37524264 37557658 5 5 5
(chronic granulomatous disease)
CYP4A11 1579 cytochrome P450, family 4, subfamily A, 1 1p33 47167433 47180004 6 5 5
polypeptide 11
CYP4F2 8529 cytochrome P450, family 4, subfamily F, 19 19pter-p13.11 15849834 15869884 15 11 11
polypeptide 2
CYP4F3 4051 cytochrome P450, family 4, subfamily F, 19 19p13.2 15612707 15632570 28 25 25
polypeptide 3
DCN 1634 decorin 12 12q21.33 90063166 90100937 6 3 3
DDX58 23586 DEAD (Asp-Glu-Ala-Asp) box 9 9p12 32445300 32516322 21 18 18
polypeptide 58
DEFB1 1672 defensin, beta 1 8 8p23.1 6715507 6722939 27 23 23
DEFB118 117285 defensin, beta 118 20 20q11.21 29420089 29424825 7 7 7
DEFB127 140850 defensin, beta 127 20 20p13 86186 87804 8 7 7
DMBT1 1755 deleted in malignant brain tumors 1 10 10q26.13 124310171 124393242 12 12 12
DOCK2 1794 dedicator of cytokinesis 2 5 5q35.1 168996871 169442959 164 160 160
DOCK3 1795 dedicator of cytokinesis 3 3 3p21.2 50687676 51396669 14 14 14
DUSP1 1843 dual specificity phosphatase 1 5 5q34 172127707 172130809 7 6 6
DUSP3 1845 dual specificity phosphatase 3 17 17q21 39199015 39211872 4 4 4
EBI3 10148 Epstein-Barr virus induced gene 3 19 19p13.3 4180540 4188525 6 6 6
EDN1 1906 endothelin 1 6 6p24.1 12398515 12405413 11 10 10
EDN2 1907 endothelin 2 1 1p34 41717033 41722884 9 9 9
EDNRA 1909 endothelin receptor type A 4 4q31.22 148621575 148685555 16 14 14
EIF2AK2 5610 eukaryotic translation initiation factor 2- 2 2p22-p21 37187203 37237572 10 10 10
alpha kinase 2
ELK1 2002 ELK1, member of ETS oncogene family X Xp11.2 47379864 47394964 4 3 3
EMD 2010 emerin (Emery-Dreifuss muscular X Xq28 153260981 153263075 1 1 1
dystrophy)
EPHB6 2051 EPH receptor B6 7 7q33-q35 142262914 142278969 10 8 8
EPHX2 2053 epoxide hydrolase 2, cytoplasmic 8 8p21 27404562 27458403 15 15 15
EPOR 2057 erythropoietin receptor 19 19p13.3-p13.2 11349475 11356019 3 3 3
ERAP1 51752 endoplasmic reticulum aminopeptidase 1 5 5q15 96122270 96169648 38 38 38
ESR1 2099 estrogen receptor 1 6 6q25.1 152170379 152466099 54 53 53
ESR2 2100 estrogen receptor 2 (ER beta) 14 14q23.2 63763504 63875021 17 17 17
ESRRA 2101 estrogen-related receptor alpha 11 11q13 63829620 63840786 5 4 4
ESRRB 2103 estrogen-related receptor beta 14 14q24.3 75907479 76036961 62 60 60
ESRRG 2104 estrogen-related receptor gamma 1 1q41 214743211 215329599 251 242 242
F10 2159 coagulation factor X 13 13q34 112825114 112851844 36 31 31
F11 2160 coagulation factor XI (plasma 4 4q35 187424112 187447829 21 21 21
thromboplastin antecedent)
F11R 50848 F11 receptor 1 1q21.2-q21.3 159232608 159275358 13 13 13
F12 2161 coagulation factor XII (Hageman factor) 5 5q33-qter 176761745 176769183 3 3 3
F13A1 2162 coagulation factor XIII, A1 polypeptide 6 6p25.3-p24.3 6089310 6265923 248 235 235
F13B 2165 coagulation factor XIII, B polypeptide 1 1q31-q32.1 195274944 195303020 10 10 10
F2 2147 coagulation factor II (thrombin) 11 11p11 46697331 46717631 9 9 9
F2R 2149 coagulation factor II (thrombin) receptor 5 5q13 76047542 76067054 17 17 17
F2RL1 2150 coagulation factor II (thrombin) receptor- 5 5q13 76150610 76166896 14 13 13
like 1
F2RL2 2151 coagulation factor II (thrombin) receptor- 5 5q13 75947063 75954996 25 25 25
like 2
F2RL3 9002 coagulation factor II (thrombin) receptor- 19 19p12 16860826 16863830 6 6 6
like 3
F3 2152 coagulation factor III (thromboplastin, 1 1p22-p21 94767461 94779903 6 5 5
tissue factor)
F5 2153 coagulation factor V (proaccelerin, labile 1 1q23 167747816 167822393 51 42 42
factor)
F7 2155 coagulation factor VII (serum 13 13q34 112808106 112822996 25 20 20
prothrombin conversion accelerator)
F8 2157 coagulation factor VIII, procoagulant X Xq28 153717260 153904192 10 9 9
component (hemophilia A)
F9 2158 coagulation factor IX (plasma X Xq27.1-q27.2 138440561 138473283 12 10 10
thromboplastic component, Christmas
disease, hemophilia B)
FADD 8772 Fas (TNFRSF6)-associated via death 11 11q13.3 69726917 69731144 4 4 4
domain
FAM132A 388581 family with sequence similarity 132, 1 1p36.33 1167696 1171965 1 1 1
member A
FAS 355 Fas (TNF receptor superfamily, member 10 10q24.1 90740268 90765522 23 21 21
6)
FASLG 356 Fas ligand (TNF superfamily, member 6) 1 1q23 170894808 170902636 11 11 10
FCER1G 2207 Fc fragment of IgE, high affinity I, 1 1q23 159451711 159455662 15 15 15
receptor for; gamma polypeptide
FCN1 2219 ficolin (collagen/fibrinogen domain 9 9q34 136941253 136949630 7 7 7
containing) 1
FCN2 2220 ficolin (collagen/fibrinogen domain 9 9q34.3 136912479 136919187 20 18 18
containing lectin) 2 (hucolin)
FCN3 8547 ficolin (collagen/fibrinogen domain 1 1p36.11 27568188 27573902 5 4 4
containing) 3 (Hakata antigen)
FES 2242 feline sarcoma oncogene 15 15q26.1 89228713 89240010 6 5 5
FGA 2243 fibrinogen alpha chain 4 4q28 155723730 155731347 13 12 12
FGB 2244 fibrinogen beta chain 4 4q28 155703596 155711688 16 14 14
FGF1 2246 fibroblast growth factor 1 (acidic) 5 5q31 141953306 142045812 36 33 33
FGG 2266 fibrinogen gamma chain 4 4q28 155744736 155753352 14 14 14
FGL2 10875 fibrinogen-like 2 7 7q11.23 76660624 76667086 7 7 7
FIGF 2277 c-fos induced growth factor (vascular Xp22.31 15273639 15312498 10 10 10
endothelial growth factor D)
FLNA 2316 filamin A, alpha (actin binding protein Xq28 153230091 153252845 0 0 0
280)
FLNB 2317 filamin B, beta (actin binding protein 3 3p14.3 57969167 58133018 37 34 34
278)
FLT1 2321 fms-related tyrosine kinase 1 (vascular 13 13q12 27774389 27967265 54 53 53
endothelial growth factor/vascular
permeability factor receptor)
FN1 2335 fibronectin 1 2 2q34 215933422 216009036 28 27 27
FOS 2353 v-fos FBJ murine osteosarcoma viral 14 14q24.3 74815284 74818666 9 8 7
oncogene homolog
FPR1 2357 formyl peptide receptor 1 19 19q13.4 56940838 56946962 17 17 17
FUK 197258 fucokinase 16 16q22.1 69045999 69071678 10 7 7
FUT3 2525 fucosyltransferase 3 (galactoside 3(4)-L- 19 19p13.3 5793899 5802485 10 7 7
fucosyltransferase, Lewis blood group)
GAB1 2549 GRB2-associated binding protein 1 4 4q31.21 144477500 144610729 17 16 16
GATA3 2625 GATA binding protein 3 10 10p15 8136673 8157170 11 11 11
GFRA1 2674 GDNF family receptor alpha 1 10 10q26.11 117812943 118022966 60 59 59
GFRA2 2675 GDNF family receptor alpha 2 8 8p21.3 23 23 23
GHR 2690 growth hormone receptor 5 5p13-p12 42459783 42757683 17 15 15
GLMN 11146 glomulin, FKBP associated protein 1 1p22.1 92484543 92537154 5 5 5
GNA12 2768 guanine nucleotide binding protein (G 7 7p22.2 2734265 2850485 20 18 18
protein) alpha 12
GNAQ 2776 guanine nucleotide binding protein (G 9 9q21 79525009 79836012 32 32 32
protein), q polypeptide
GP1BA 2811 glycoprotein Ib (platelet), alpha 17 17pter-p12 4776372 4779067 6 6 6
polypeptide
GP1BB 2812 glycoprotein Ib (platelet), beta 22 22g11.21-q11.23| 18091066 18092297 5 5 5
polypeptide 22q11.21
GP5 2814 glycoprotein V (platelet) 3 3q29 195596839 195601284 4 4 4
GP6 51206 glycoprotein VI (platelet) 19 19q13.4 60216885 60241444 16 16 16
GP9 2815 glycoprotein IX (platelet) 3 3q21.3 130262335 130263939 2 1 1
GPI 2821 glucose phosphate isomerase 19 19q13.1 39547909 39583076 5 5 5
GPR44 11251 G protein-coupled receptor 44 11 11q12-q13.3 60374974 60380020 6 6 6
GPR68 8111 G protein-coupled receptor 68 14 14q31 90768629 90789977 11 9 9
GRB2 2885 growth factor receptor-bound protein 2 17 17q24-q25 70825752 70913385 10 10 10
GYPC 2995 glycophorin C (Gerbich blood group) 2 2q14-q21 127130154 127170716 32 30 30
HABP2 3026 hyaluronan binding protein 2 10 10q25.3 115302775 115339348 50 48 48
HCK 3055 hemopoietic cell kinase 20 20q11-q12 30103718 30153320 11 9 9
HDAC4 9759 histone deacetylase 4 2 2q37.3 239634801 239987580 105 102 101
HDAC5 10014 histone deacetylase 5 17 17q21 39509647 39556540 8 8 8
HDAC7 51564 histone deacetylase 7 12 12q13.1 46462772 46499924 13 13 13
HDAC9 9734 histone deacetylase 9 7 7p21.1 18501894 19003518 177 170 170
HGF 3082 hepatocyte growth factor (hepapoietin A; 7 7q21.1 81169380 81237388 18 17 17
scatter factor)
HLA-A 3105 major histocompatibility complex, class I, A 6 6p21.3 30018310 30021633 27 9 9
HLA-B 3106 major histocompatibility complex, class I, B 6 6p21.3 31429628 31432914 29 20 20
HLA-C 3107 major histocompatibility complex, class I, C 6 6p21.3 31344508 31347834 47 33 33
HLA- 3108 major histocompatibility complex, class 6 6p21.3 33024373 33028831 14 13 13
DMA II, DM alpha
HLA- 3109 major histocompatibility complex, class 6 6p21.3 33010393 33016795 22 22 22
DMB II, DM beta
HLA- 3111 major histocompatibility complex, class 6 6p21.3 33079937 33085367 15 15 15
DOA II, DO alpha
HLA- 3112 major histocompatibility complex, class 6 6p21.3 32888518 32892803 22 22 22
DOB II, DO beta
HLA- 3113 major histocompatibility complex, class 6 6p21.3 33140772 33149356 23 17 17
DPA1 II, DP alpha 1
HLA- 3115 major histocompatibility complex, class 6 6p21.3 33151738 33162954 28 23 23
DPB1 II, DP beta 1
HLA- 3118 major histocompatibility complex, class 6 6p21.3 32817141 32823199 24 20 20
DQA2 II, DQ alpha 2
HLA- 3119 major histocompatibility complex, class 6 6p21.3 32735635 32742444 1 1 1
DQB1 II, DQ beta 1
HLA- 3120 major histocompatibility complex, class 6 6p21 32831853 32839308 27 24 24
DQB2 II, DQ beta 2
HLA- 3122 major histocompatibility complex, class 6 6p21.3 32515625 32520801 15 15 15
DRA II, DR alpha
HLA- 3125 major histocompatibility complex, class 6 6p21.3 0 0 0
DRB3 II, DR beta 3
HLA- 3126 major histocompatibility complex, class 6 6p21.3 0 0 0
DRB4 II, DR beta 4
HLA- 3127 major histocompatibility complex, class 6 6p21.3 32593129 32605984 1 0 0
DRB5 II, DR beta 5
HLA-E 3133 major histocompatibility complex, class I, E 6 6p21.3 30565250 30569077 8 7 7
HLA-F 3134 major histocompatibility complex, class I, F 6 6p21.3 29799096 29803052 14 13 13
HLA-G 3135 major histocompatibility complex, class I, G 6 6p21.3 29903497 29906859 11 11 11
HLA-H 3136 major histocompatibility complex, class I, 6 6p21.3 29963508 29966245 7 3 3
H (pseudogene)
HMOX1 3162 heme oxygenase (decycling) 1 22 22q12|22q13.1 34107087 34120194 10 10 10
HRG 3273 histidine-rich glycoprotein 3 3q27 187866492 187878717 16 14 14
HRH1 3269 histamine receptor H1 3 3p25 11153779 11279939 5 5 5
HSP90B1 7184 heat shock protein 90 kDa beta (Grp94), 12 12q24.2-q24.3 102848319 102865833 24 24 24
member 1
HSPA14 51182 heat shock 70 kDa protein 14 10 10p13 14920267 14953746 6 6 6
HSPG2 3339 heparan sulfate proteoglycan 2 1 1p36.1-p34 22021324 22136337 20 20 20
HTR1A 3350 5-hydroxytryptamine (serotonin) receptor 5 5q11.2-q13 63292034 63293302 4 4 4
1A
HTRA2 27429 HtrA serine peptidase 2 2 2p12 74610040 74614191 3 3 3
ICAM1 3383 intercellular adhesion molecule 1 (CD54), 19 19p13.3-p13.2 10242779 10258291 11 10 10
human rhinovirus receptor
ICAM2 3384 intercellular adhesion molecule 2 17 17q23-q25 59433687 59451726 4 3 3
ICEBERG 59082 ICEBERG caspase-1 inhibitor 11 11q22.3 104513879 104515663 4 4 4
IER3 8870 immediate early response 3 6 6p21.3 30818955 30820306 3 3 3
IFI16 3428 interferon, gamma-inducible protein 16 1 1q22 157246306 157291569 13 12 12
IFNA1 3439 interferon, alpha 1 9 9p22 21430440 21431315 6 5 5
IFNA2 3440 interferon, alpha 2 9 9p22 21374254 21375396 5 5 5
IFNAR1 3454 interferon (alpha, beta and omega) 21 21q22.1|21q22.11 33619084 33653999 9 9 9
receptor 1
IFNAR2 3455 interferon (alpha, beta and omega) 21 21q22.1|21q22.11 33524101 33558697 17 14 14
receptor 2
IFNB1 3456 interferon, beta 1, fibroblast 9 9p21 21067104 21067943 6 6 6
IFNG 3458 interferon, gamma 12 12q14 66834817 66839788 6 6 6
IFNGR1 3459 interferon gamma receptor 1 6 6q23.3 137560315 137582200 11 9 9
IFNGR2 3460 interferon gamma receptor 2 (interferon 21 21q22.11 33697072 33731696 11 9 9
gamma transducer 1)
IFT57 55081 intraflagellar transport 57 homolog 3 3q13.13 109362349 109423938 12 12 12
(Chlamydomonas)
IGF1 3479 insulin-like growth factor 1 12 12q23.2 101313806 101398454 17 15 15
(somatomedin C)
IKBKAP 8518 inhibitor of kappa light polypeptide gene 9 9q31 110669621 110736217 42 42 42
enhancer in B-cells, kinase complex-
associated protein
IKBKB 3551 inhibitor of kappa light polypeptide gene 8 8p11.2 42247986 42309122 10 8 8
enhancer in B-cells, kinase beta
IKBKE 9641 inhibitor of kappa light polypeptide gene 1 1q32.1 204710419 204736845 25 22 22
enhancer in B-cells, kinase epsilon
IKBKG 8517 inhibitor of kappa light polypeptide gene X Xq28 153423653 153446455 2 2 2
enhancer in B-cells, kinase gamma
IL10 3586 interleukin 10 1 1q31-q32 205007571 205012462 11 11 11
IL10RA 3587 interleukin 10 receptor, alpha 11 11q23 117362319 117377404 18 16 15
IL10RB 3588 interleukin 10 receptor, beta 21 21q22.1-q22.2| 33560542 33591390 19 18 18
21q22.11
IL11 3589 interleukin 11 19 19q13.3-q13.4 60567569 60573626 9 8 8
IL11RA 3590 interleukin 11 receptor, alpha 9 9p13 34643932 34651884 5 4 4
IL12A 3592 interleukin 12A (natural killer cell 3 3q25.33-q26 161189323 161196500 12 12 12
stimulatory factor 1, cytotoxic
lymphocyte maturation factor 1, p35)
IL12B 3593 interleukin 12B (natural killer cell 5 5q31.1-q33.1 158674369 158690059 16 16 16
stimulatory factor 2, cytotoxic
lymphocyte maturation factor 2, p40)
IL12RB1 3594 interleukin 12 receptor, beta 1 19 19p13.1 18031371 18058697 15 12 12
IL12RB2 3595 interleukin 12 receptor, beta 2 1 1p31.3-p31.2 67545635 67635171 21 20 20
IL13 3596 interleukin 13 5 5q31 132021764 132024700 7 6 6
IL13RA1 3597 interleukin 13 receptor, alpha 1 X Xq24 117745587 117812524 5 5 5
IL13RA2 3598 interleukin 13 receptor, alpha 2 X Xq13.1-q28 114144794 114158463 3 2 2
IL15RA 3601 interleukin 15 receptor, alpha 10 10p15.1 6034340 6060148 32 29 29
IL16 3603 interleukin 16 (lymphocyte 15 15q26.3 79276274 79392157 27 25 25
chemoattractant factor)
IL17A 3605 interleukin 17A 6 6p12 52159144 52163395 13 13 13
IL17B 27190 interleukin 17B 5 5q33.1 148734023 148739031 6 5 5
IL17C 27189 interleukin 17C 16 16q24 87232502 87234383 7 7 7
IL17D 53342 interleukin 17D 13 13q12.11 20175482 20195237 7 6 6
IL17F 112744 interleukin 17F 6 6p12 52209443 52217257 14 14 14
IL17RB 55540 interleukin 17 receptor B 3 3p21.1 53855617 53874867 10 9 9
IL18 3606 interleukin 18 (interferon-gamma- 11 11q22.2-q22.3 111519186 111540050 6 6 6
inducing factor)
IL18R1 8809 interleukin 18 receptor 1 2 2q12 102345529 102381650 15 14 14
IL18RAP 8807 interleukin 18 receptor accessory protein 2 2q12 102401686 102435457 15 15 15
IL19 29949 interleukin 19 1 1q32.2 205038838 205082948 18 18 18
IL1A 3552 interleukin 1, alpha 2 2q14 113247963 113259442 9 9 9
IL1B 3553 interleukin 1, beta 2 2q14 113303808 113310827 8 8 8
IL1F10 84639 interleukin 1 family, member 10 (theta) 2 2q13 113542018 113549898 25 24 24
IL1F5 26525 interleukin 1 family, member 5 (delta) 2 2q14 113532686 113538792 20 20 20
IL1F6 27179 interleukin 1 family, member 6 (epsilon) 2 2q12-q14.1 113479920 113482092 9 6 6
IL1F7 27178 interleukin 1 family, member 7 (zeta) 2 2q12-q14.1 113387019 113392930 10 10 10
IL1F8 27177 interleukin 1 family, member 8 (eta) 2 2q14 113496139 113526911 14 11 11
IL1F9 56300 interleukin 1 family, member 9 2 2q12-q21 113452077 113459698 7 7 7
IL1R1 3554 interleukin 1 receptor, type I 2 2q12 102136834 102162766 25 20 20
IL1R2 7850 interleukin 1 receptor, type II 2 2q12 101974738 102011317 17 15 15
IL1RAP 3556 interleukin 1 receptor accessory protein 3 3q28 191714585 191851995 59 54 54
IL1RAPL2 26280 interleukin 1 receptor accessory protein- X Xq22 103697652 104898478 39 37 37
like 2
IL1RL1 9173 interleukin 1 receptor-like 1 2 2q12 102294394 102334929 21 20 20
IL1RL2 8808 interleukin 1 receptor-like 2 2 2q12 102169865 102222243 23 22 22
IL1RN 3557 interleukin 1 receptor antagonist 2 2q14.2 113591941 113608064 16 16 16
IL2 3558 interleukin 2 4 4q26-q27 123592075 123597100 4 4 4
IL20 50604 interleukin 20 1 1q32 205105777 205109191 5 5 5
IL20RA 53832 interleukin 20 receptor, alpha 6 6q23.3 137362801 137407991 13 13 13
IL21 59067 interleukin 21 4 4q26-q27 123739272 123761662 6 6 6
IL21R 50615 interleukin 21 receptor 16 16p11 27321224 27369616 25 24 24
IL22 50616 interleukin 22 12 12q15 66928292 66933548 12 12 12
IL22RA1 58985 interleukin 22 receptor, alpha 1 1 1p36.11 24318848 24342198 21 20 20
IL22RA2 116379 interleukin 22 receptor, alpha 2 6 6q25.1 137506650 137536478 13 12 12
IL23R 149233 interleukin 23 receptor 1 1p31.3 67404757 67498250 30 29 29
IL24 11009 interleukin 24 1 1q32 205137412 205144107 2 2 2
IL25 64806 interleukin 25 14 14q11.2 22911858 22915452 9 9 9
IL26 55801 interleukin 26 12 12q15 66881396 66905838 14 11 11
IL27 246778 interleukin 27 16 16p11 28418184 28425656 1 1 1
IL28RA 163702 interleukin 28 receptor, alpha (interferon, 1 1p36.11 24353234 24386338 19 18 18
lambda receptor)
IL2RA 3559 interleukin 2 receptor, alpha 10 10p15-p14 6093512 6144278 43 41 41
IL2RB 3560 interleukin 2 receptor, beta 22 22q13|22q13.1 35851824 35875908 22 20 20
IL2RG 3561 interleukin 2 receptor, gamma (severe X Xq13.1 70243984 70248128 5 5 5
combined immunodeficiency)
IL3 3562 interleukin 3 (colony-stimulating factor, 5 5q31.1 131424246 131426795 6 6 6
multiple)
IL31RA 133396 interleukin 31 receptor A 5 5q11.2 55183091 55248738 18 18 18
IL32 9235 interleukin 32 16 16p13.3 3055314 3059669 8 7 7
IL3RA 3563 interleukin 3 receptor, alpha (low affinity) X|Y Xp22.3 or 12 5 5
Yp11.3
IL4 3565 interleukin 4 5 5q31.1 132037272 132046267 8 7 7
IL4R 3566 interleukin 4 receptor 16 16p12.1-p11.2 27232752 27283600 24 24 24
IL5 3567 interleukin 5 (colony-stimulating factor, 5 5q31.1 131905035 131907113 6 5 5
eosinophil)
IL5RA 3568 interleukin 5 receptor, alpha 3 3p26-p24 3086421 3127031 44 44 44
IL6 3569 interleukin 6 (interferon, beta 2) 7 7p21 22733343 22738145 11 11 11
IL6ST 3572 interleukin 6 signal transducer (gp130, 5 5q11 55272451 55326520 8 7 7
oncostatin M receptor)
IL7 3574 interleukin 7 8 8q12-q13 79807560 79880313 12 12 12
IL7R 3575 interleukin 7 receptor 5 5p13 35892748 35912681 14 13 13
IL8 3576 interleukin 8 4 4q13-q21 74825139 74828297 3 2 2
IL8RA 3577 interleukin 8 receptor, alpha 2 2q35 218735813 218739961 7 6 6
IL8RB 3579 interleukin 8 receptor, beta 2 2q35 218698991 218710220 5 4 4
IL9 3578 interleukin 9 5 5q31.1 135255834 135259415 9 7 7
IL9R 3581 interleukin 9 receptor X|Y Xq28 and 5 3 3
Yq12
IMMT 10989 inner membrane protein, mitochondrial 2 2p11.2|2 86224566 86276404 12 12 11
(mitofilin)
INHA 3623 inhibin, alpha 2 2q33-q36 220145198 220148671 6 5 5
INHBA 3624 inhibin, beta A 7 7p15-p13 41695126 41709231 7 7 7
INHBB 3625 inhibin, beta B 2 2cen-q13 120820189 120825853 7 7 7
INPP5D 3635 inositol polyphosphate-5-phosphatase, 2 2q37.1 23 23 23
145 kDa
INS 3630 insulin 11 11p15.5 2137585 2139015 4 4 4
IRAK1 3654 interleukin-1 receptor-associated kinase 1 X Xq28 152929151 152938536 1 1 1
IRAK2 3656 interleukin-1 receptor-associated kinase 2 3 3p25.3 10181563 10260427 23 22 22
IRAK3 11213 interleukin-1 receptor-associated kinase 3 12 12q14.3 64869284 64928652 10 9 9
IRAK4 51135 interleukin-1 receptor-associated kinase 4 12 12q12 42439047 42468166 7 7 7
IRF1 3659 interferon regulatory factor 1 5 5q31.1 131846679 131854326 7 7 7
IRF3 3661 interferon regulatory factor 3 19 19q13.3-q13.4 54854641 54860936 2 2 2
IRF4 3662 interferon regulatory factor 4 6 6p25-p23 336760 356193 14 12 12
IRF7 3665 interferon regulatory factor 7 11 11p15.5 602555 605999 8 8 8
IRF8 3394 interferon regulatory factor 8 16 16q24.1 84490275 84513713 32 32 32
IRF9 10379 interferon regulatory factor 9 14 14q11.2 23700262 23705614 6 5 5
IRS2 8660 insulin receptor substrate 2 13 13q34 109204185 109236915 16 16 16
ITCH 83737 itchy E3 ubiquitin protein ligase homolog 20 20q11.22 32414745 32562858 8 6 6
(mouse)
ITGA1 3672 integrin, alpha 1 5 5q11.2 52119893 52285242 77 75 75
ITGA2 3673 integrin, alpha 2 (CD49B, alpha 2 subunit 5 5q23-q31 52320913 52426366 53 47 47
of VLA-2 receptor)
ITGA2B 3674 integrin, alpha 2b (platelet glycoprotein 17 17q21.32 39805076 39822399 4 4 4
IIb of IIb/IIIa complex, antigen CD41)
ITGA4 3676 integrin, alpha 4 (antigen CD49D, alpha 4 2 2q31.3 182029864 182110719 27 27 27
subunit of VLA-4 receptor)
ITGA5 3678 integrin, alpha 5 (fibronectin receptor, 12 12q11-q13 53075312 53099317 3 3 3
alpha polypeptide)
ITGA6 3655 integrin, alpha 6 2 2q31.1 173000560 173079427 23 20 20
ITGA8 8516 integrin, alpha 8 10 10p13 15599094 15801776 41 39 39
ITGAD 3681 integrin, alpha D 16 16p11.2 31312134 31345327 6 6 6
ITGAL 3683 integrin, alpha L (antigen CD11A (p180), 16 16p11.2 30391572 30442007 17 17 17
lymphocyte function-associated antigen
1; alpha polypeptide)
ITGAM 3684 integrin, alpha M (complement 16 16p11.2 31178789 31251714 9 9 9
component 3 receptor 3 subunit)
ITGAV 3685 integrin, alpha V (vitronectin receptor, 2 2q31-q32 187163045 187253873 20 20 20
alpha polypeptide, antigen CD51)
ITGAX 3687 integrin, alpha X (complement 16 16p11.2 31274010 31301819 11 11 11
component 3 receptor 4 subunit)
ITGB1 3688 integrin, beta 1 (fibronectin receptor, beta 10 10p11.2 33229326 33287204 20 19 19
polypeptide, antigen CD29 includes
MDF2, MSK12)
ITGB1BP1 9270 integrin beta 1 binding protein 1 2 2p25.2 9463264 9481094 5 5 5
ITGB2 3689 integrin, beta 2 (complement component 21 21q22.3 45130296 45165303 26 24 24
3 receptor 3 and 4 subunit)
ITGB3 3690 integrin, beta 3 (platelet glycoprotein IIIa, 17 17q21.32 42686207 42745076 23 21 21
antigen CD61)
ITGB3BP 23421 integrin beta 3 binding protein (beta3- 1 1p31.3 63679050 63761423 13 12 12
endonexin)
ITGB7 3695 integrin, beta 7 12 12q13.13 51871374 51887267 5 4 4
ITIH4 3700 inter-alpha (globulin) inhibitor H4 3 3p21.1 52822046 52839734 9 8 8
(plasma Kallikrein-sensitive
glycoprotein)
ITPR1 3708 inositol 1,4,5-triphosphate receptor, type 1 3 3p26.1 4510034 4864286 178 174 173
JAK2 3717 Janus kinase 2 (a protein tyrosine kinase) 9 9p24 4975245 5117995 18 15 15
JAK3 3718 Janus kinase 3 (a protein tyrosine kinase, 19 19p13.1 17797961 17819800 17 16 16
leukocyte)
JUN 3725 jun oncogene 1 1p32-p31 59019051 59022373 4 4 4
KEL 3792 Kell blood group, metallo-endopeptidase 7 7q33 142348323 142369625 6 6 6
KLHDC2 23588 kelch domain containing 2 14 14q21.3 49304537 49319606 1 0 0
KLK1 3816 kallikrein 1 19 19q13.3 56014216 56018855 14 13 13
KLK3 354 kallikrein-related peptidase 3 19 19q13.41 56049983 56055832 16 14 14
KLKB1 3818 kallikrein B, plasma (Fletcher factor) 1 4 4q35 187385666 187416619 20 19 19
KNG1 3827 kininogen 1 3 3q27 187917814 187944437 25 24 24
L1RE1 4029 LINE1 retrotransposable element 1 22 22q11.1-q11.2 0 0 0
L1RE2 4030 LINE1 retrotransposable element 2 1 1q 0 0 0
LBP 3929 lipopolysaccharide binding protein 20 20q11.23 36408299 36439067 20 19 19
LEP 3952 leptin 7 7q31.3 127668567 127684917 6 6 6
LEPR 3953 leptin receptor 1 1p31 65658906 65875410 37 37 37
LIFR 3977 leukemia inhibitory factor receptor alpha 5 5p13-p12 38510822 38631253 12 12 12
LRP1 4035 low density lipoprotein-related protein 1 12 12q13-q14 55808549 55893409 14 13 13
(alpha-2-macroglobulin receptor)
LTA 4049 lymphotoxin alpha (TNF superfamily, 6 6p21.3 31648072 31650077 16 13 13
member 1)
LTA4H 4048 leukotriene A4 hydrolase 12 12q22 94918742 94953496 22 22 22
LTB 4050 lymphotoxin beta (TNF superfamily, 6 6p21.3 31656314 31658181 17 13 13
member 3)
LTB4R 1241 leukotriene B4 receptor 14 14q11.2-q12 23852357 23855992 6 6 6
LTBR 4055 lymphotoxin beta receptor (TNFR 12 12p13 6363618 6370993 5 4 4
superfamily, member 3)
LTF 4057 lactotransferrin 3 3p21.31 46452500 46481399 8 8 8
LY75 4065 lymphocyte antigen 75 2 2q24 160368112 160469508 27 27 27
LY86 9450 lymphocyte antigen 86 6 6p25.1 6533933 6600215 46 44 44
LY9 4063 lymphocyte antigen 9 1 1q23.3 159032552 159064669 8 8 8
LY96 23643 lymphocyte antigen 96 8 8q21.11 75066144 75103859 16 15 15
MADD 8567 MAP-kinase activating death domain 11 11p11.2 47247535 47308158 8 8 8
MAP2K3 5606 mitogen-activated protein kinase kinase 3 17 17q11.2 21128561 21159145 7 5 5
MAP2K4 6416 mitogen-activated protein kinase kinase 4 17 17p11.2 11864860 11987776 19 18 18
MAP3K1 4214 mitogen-activated protein kinase kinase 5 5q11.2 56146657 56227736 17 17 17
kinase 1
MAP3K14 9020 mitogen-activated protein kinase kinase 17 17q21 40696271 40750197 8 8 8
kinase 14
MAP3K3 4215 mitogen-activated protein kinase kinase 17 17q23.3 59053533 59127402 7 7 7
kinase 3
MAP3K7 6885 mitogen-activated protein kinase kinase 6 6q15 91282074 91353628 12 12 12
kinase 7
MAP3K7IP1 10454 mitogen-activated protein kinase kinase 22 22q13.1 38125705 38163078 4 4 4
kinase 7 interacting protein 1
MAP3K8 1326 mitogen-activated protein kinase kinase 10 10p11.23 30762872 30790767 9 8 8
kinase 8
MAP4K4 9448 mitogen-activated protein kinase kinase 2 2q11.2-q12 101680920 101877584 20 20 20
kinase kinase 4
MAPK1 5594 mitogen-activated protein kinase 1 22 22q11.2|22q11.21 20443946 20551970 8 7 6
MAPK11 5600 mitogen-activated protein kinase 11 22 22q13.33 49044269 49050906 9 7 7
MAPK14 1432 mitogen-activated protein kinase 14 6 6p21.3-p21.2 36103551 36186513 15 13 13
MAPK3 5595 mitogen-activated protein kinase 3 16 16p11.2 30032927 30042131 4 4 4
MAPK6 5597 mitogen-activated protein kinase 6 15 15q21 50098739 50145754 7 7 7
MAPK8 5599 mitogen-activated protein kinase 8 10 10q11.22 49279693 49313189 10 10 10
MAPK9 5601 mitogen-activated protein kinase 9 5 5q35 179595390 179640216 21 20 20
MAPKAPK2 9261 mitogen-activated protein kinase- 1 1q32 204924912 204974249 13 11 11
activated protein kinase 2
MASP1 5648 mannan-binding lectin serine peptidase 1 3 3q27-q28 188418632 188492446 51 49 49
(C4/C2 activating component of Ra-
reactive factor)
MASP2 10747 mannan-binding lectin serine peptidase 2 1 1p36.3-p36.2 11009167 11029872 3 3 3
MBL2 4153 mannose-binding lectin (protein C) 2, 10 10q11.2 54195146 54201466 20 18 18
soluble (opsonic defect)
MBL3P 50639 mannose-binding lectin (protein A) 1, 10 10q22.3 0 0 0
pseudogenemannose-binding lectin
family member 3, pseudogene
MEFV 4210 Mediterranean fever 16 16p13.3 3232029 3246628 8 8 8
MEN1 4221 multiple endocrine neoplasia I 11 11q13 64327564 64335342 4 4 4
MGLL 11343 monoglyceride lipase 3 3q21.3 128890599 129024741 33 31 31
MIF 4282 macrophage migration inhibitory factor 22 22q11.23 22566565 22567409 10 10 10
(glycosylation-inhibiting factor)
MMP1 4312 matrix metallopeptidase 1 (interstitial 11 11q22.3 102165861 102174104 17 16 16
collagenase)
MMP2 4313 matrix metallopeptidase 2 (gelatinase A, 16 16q13-q21 54070589 54098104 17 16 16
72 kDa gelatinase, 72 kDa type IV
collagenase)
MMP25 64386 matrix metallopeptidase 25 16 16p13.3 3036683 3050728 10 9 9
MMP3 4314 matrix metallopeptidase 3 (stromelysin 1, 11 11q22.3 102211738 102219552 11 10 10
progelatinase)
MMP9 4318 matrix metallopeptidase 9 (gelatinase B, 20 20q11.2-q13.1 44070954 44078607 10 10 10
92 kDa gelatinase, 92 kDa type IV
collagenase)
MMRN1 22915 multimerin 1 4 4q22 91035075 91094803 12 12 12
MPL 4352 myeloproliferative leukemia virus 1 1p34 43576062 43592722 4 4 4
oncogene
MTHFR 4524 5,10-methylenetetrahydrofolate reductase 1 1p36.3 11768374 11788702 19 17 17
(NADPH)
MTR 4548 5-methyltetrahydrofolate-homocysteine 1 1q43 235025341 235130585 13 11 11
methyltransferase
MYD88 4615 myeloid differentiation primary response 3 3p22 38155009 38159517 5 5 5
gene (88)
NAIP 4671 NLR family, apoptosis inhibitory protein 5 5q13.1 70300066 70356697 0 0 0
NCAM1 4684 neural cell adhesion molecule 1 11 11q23.1 112337205 112654368 75 74 74
NCOA4 8031 nuclear receptor coactivator 4 10 10q11.2 51242373 51260738 7 7 7
NCOR2 9612 nuclear receptor co-repressor 2 12 12q24 123374914 123586102 51 50 50
NCR3 259197 natural cytotoxicity triggering receptor 3 6 6p21.3 31664651 31668741 6 5 5
NEBL 10529 nebulette 10 10p12 21110093 21503122 79 73 73
NFAM1 150372 NFAT activating protein with ITAM 22 22q13.2 41106357 41158345 19 18 18
motif 1
NFATC3 4775 nuclear factor of activated T-cells, 16 16q22.2 66676876 66818338 5 5 5
cytoplasmic, calcineurin-dependent 3
NFATC4 4776 nuclear factor of activated T-cells, 14 14q11.2 23907094 23918650 9 9 9
cytoplasmic, calcineurin-dependent 4
NFE2 4778 nuclear factor (erythroid-derived 2), 12 12q13 52972162 52975811 3 3 3
45 kDa
NFE2L1 4779 nuclear factor (erythroid-derived 2)-like 1 17 17q21.3 43480745 43493841 8 7 7
NFIL3 4783 nuclear factor, interleukin 3 regulated 9 9q22 93211148 93225965 7 7 7
NFKB1 4790 nuclear factor of kappa light polypeptide 4 4q24 103641518 103757507 18 16 16
gene enhancer in B-cells 1 (p105)
NFKB2 4791 nuclear factor of kappa light polypeptide 10 10q24 104144219 104152271 4 4 4
gene enhancer in B-cells 2 (p49/p100)
NFKBIA 4792 nuclear factor of kappa light polypeptide 14 14q13 34940468 34943695 12 11 10
gene enhancer in B-cells inhibitor, alpha
NFKBIB 4793 nuclear factor of kappa light polypeptide 19 19q13.1 44082455 44091374 9 8 8
gene enhancer in B-cells inhibitor, beta
NFKBIE 4794 nuclear factor of kappa light polypeptide 6 6p21.1 44333881 44341503 6 5 5
gene enhancer in B-cells inhibitor,
epsilon
NFKBIL1 4795 nuclear factor of kappa light polypeptide 6 6p21.3 31623351 31634585 13 12 12
gene enhancer in B-cells inhibitor-like 1
NFRKB 4798 nuclear factor related to kappaB binding 11 11q24-q25 129239568 129268114 11 10 10
protein
NFX1 4799 nuclear transcription factor, X-box 9 9p13.3 33280510 33361155 9 9 9
binding 1
NLRP12 91662 NLR family, pyrin domain containing 12 19 19q13.42 58988650 59019404 22 21 21
NLRP3 114548 NLR family, pyrin domain containing 3 1 1q44 245646098 245679033 32 30 30
NMI 9111 N-myc (and STAT) interactor 2 2q23 151835231 151854620 8 8 8
NOS2A 4843 nitric oxide synthase 2A (inducible, 17 17q11.2-q12 23107919 23151682 31 26 26
hepatocytes)
NOS3 4846 nitric oxide synthase 3 (endothelial cell) 7 7q36 150319080 150342609 15 13 13
NOX5 79400 NADPH oxidase, EF-hand calcium 15 15q23 67009918 67136127 12 11 11
binding domain 5
NPPB 4879 natriuretic peptide precursor B 1 1p36.2 11840108 11841579 9 9 9
NPR1 4881 natriuretic peptide receptor A/guanylate 1 1q21-q22 151917737 151933088 3 3 3
cyclase A (atrionatriuretic peptide
receptor A)
NR3C1 2908 nuclear receptor subfamily 3, group C, 5 5q31.3 142637689 142795270 14 13 13
member 1 (glucocorticoid receptor)
NR4A2 4929 nuclear receptor subfamily 4, group A, 2 2q22-q23 156889195 156897446 5 5 5
member 2
OCLN 4950 occludin 5 5q13.1 68823875 68885889 0 0 0
OLR1 4973 oxidized low density lipoprotein (lectin- 12 12p13.2-p12.3 10202166 10216057 12 10 10
like) receptor 1
OSMR 9180 oncostatin M receptor 5 5p13.1 38881893 38970159 19 18 18
P2RX1 5023 purinergic receptor P2X, ligand-gated ion 17 17p13.3 3746634 3766709 20 17 17
channel, 1
P2RY1 5028 purinergic receptor P2Y, G-protein 3 3q25.2 154035426 154038535 2 2 1
coupled, 1
P4HB 5034 procollagen-proline, 2-oxoglutarate 4- 17 17q25 77394323 77411833 2 2 2
dioxygenase (proline 4-hydroxylase), beta
polypeptide
PAFAH2 5051 platelet-activating factor acetylhydrolase 1 1p36 26158845 26197235 5 5 5
2, 40 kDa
PARP4 143 poly (ADP-ribose) polymerase family, 13 13q11 23893069 23984948 33 26 26
member 4
PAWR 5074 PRKC, apoptosis, WT1, regulator 12 12q21 78509876 78608921 4 4 4
PAX5 5079 paired box 5 9 9p13 36828531 37024476 83 78 78
PCSK9 255738 proprotein convertase subtilisin/kexin 1 1p32.3 55277808 55303111 32 31 31
type 9
PDAP1 11333 PDGFA associated protein 1 7 7q22.1 98830525 98844228 4 4 4
PECAM1 5175 platelet/endothelial cell adhesion 17 17q23 59753595 59817743 11 10 10
molecule (CD31 antigen)
PELI1 57162 pellino homolog 1 (Drosophila) 2 2p13.3 64173499 64192987 11 10 10
PELO 53918 pelota homolog (Drosophila) 5 5q11.2 52119531 52134208 10 10 10
PF4 5196 platelet factor 4 (chemokine (C—X—C 4 4q12-q21 75065660 75066541 8 7 7
motif) ligand 4)
PGLYRP1 8993 peptidoglycan recognition protein 1 19 19q13.2-q13.3 51214281 51218163 6 6 6
PGLYRP2 114770 peptidoglycan recognition protein 2 19 19p13.12 15440456 15451315 7 5 5
PGLYRP3 114771 peptidoglycan recognition protein 3 1 1q21 151536962 151549818 5 5 5
PGR 5241 progesterone receptor 11 11q22-q23 100414313 100506465 21 20 20
PIGR 5284 polymeric immunoglobulin receptor 1 1q31-q41 205168495 205186430 6 6 6
PLA2G2A 5320 phospholipase A2, group IIA (platelets, 1 1p35 20174518 20179496 14 13 13
synovial fluid)
PLA2G2D 26279 phospholipase A2, group IID 1 1p36.12 20311019 20318595 19 18 18
PLA2G4C 8605 phospholipase A2, group IVC (cytosolic, 19 19q13.3 53242917 53305826 40 35 35
calcium-independent)
PLA2G7 7941 phospholipase A2, group VII (platelet- 6 6p21.2-p12 46780237 46811061 14 14 14
activating factor acetylhydrolase, plasma)
PLAT 5327 plasminogen activator, tissue 8 8p12 42151393 42184351 35 30 30
PLAU 5328 plasminogen activator, urokinase 10 10q24 75340896 75347261 6 6 5
PLAUR 5329 plasminogen activator, urokinase receptor 19 19q13 48842088 48866342 19 16 16
PLCB1 23236 phospholipase C, beta 1 20 20p12 8061296 8813547 240 233 233
(phosphoinositide-specific)
PLCG2 5336 phospholipase C, gamma 2 16 16q24.1 80362768 80549400 123 119 119
(phosphatidylinositol-specific)
PLG 5340 plasminogen 6 6q26 161043273 161094328 60 53 53
PLSCR1 5359 phospholipid scramblase 1 3 3q23 147715658 147745186 20 19 19
PLSCR4 57088 phospholipid scramblase 4 3 3q24 147392816 147451560 22 22 22
PLTP 5360 phospholipid transfer protein 20 20q13.12 43960804 43974193 11 8 8
PLUNC 51297 palate, lung and nasal epithelium 20 20q11.2 31287463 31294773 4 4 4
associated
PON1 5444 paraoxonase 1 7 7q21.3 94764924 94791780 32 30 30
PON2 5445 paraoxonase 2 7 7q21.3 94872110 94902320 20 16 16
PON3 5446 paraoxonase 3 7 7q21.3 94827120 94863623 11 10 10
POU2AF1 5450 POU class 2 associating factor 1 11 11q23.1 110728190 110755626 13 13 13
POU2F2 5452 POU class 2 homeobox 2 19 19q13.2 47284490 47328470 6 6 6
PPARA 5465 peroxisome proliferator-activated 22 22q12-q13.1| 44925163 45018317 15 14 14
receptor alpha 22q13.31
PPARG 5468 peroxisome proliferator-activated 3 3p25 12304349 12450855 27 27 27
receptor gamma
PPBP 5473 pro-platelet basic protein (chemokine (C- 4 4q12-q13 75071619 75072764 9 6 6
X-C motif) ligand 7)
PRDX5 25824 peroxiredoxin 5 11 11q13 63842145 63845859 5 5 5
PREX1 57580 phosphatidylinositol 3,4,5-trisphosphate- 20 20q13.13 46674200 46877827 55 54 53
dependent RAC exchanger 1
PRG2 5553 proteoglycan 2, bone marrow (natural 11 11q12 56911410 56914706 6 6 6
killer cell activator, eosinophil granule
major basic protein)
PRG3 10394 proteoglycan 3 11 11q12 56900819 56905199 5 5 5
PRKAR1A 5573 protein kinase, cAMP-dependent, 17 17q23-q24 64019705 64040506 6 6 6
regulatory, type I, alpha (tissue specific
extinguisher 1)
PRKCA 5578 protein kinase C, alpha 17 17q22-q23.2 61729388 62237324 153 147 146
PRKCB1 5579 protein kinase C, beta 1 16 16p11.2 23754823 24139063 103 101 101
PRLR 5618 prolactin receptor 5 5p13.2 35099985 35266334 39 39 39
PROC 5624 protein C (inactivator of coagulation 2 2q13-q14 127892487 127903288 25 23 23
factors Va and VIIIa)
PROCR 10544 protein C receptor, endothelial (EPCR) 20 20q11.2 33223435 33228826 6 5 5
PROK2 60675 prokineticin 2 3 3p13 71903497 71916902 10 10 10
PROS1 5627 protein S (alpha) 3 3q11.2 95074647 95175395 17 17 17
PROZ 8858 protein Z, vitamin K-dependent plasma 13 13q34 112860969 112874695 22 20 20
glycoprotein
PTAFR 5724 platelet-activating factor receptor 1 1p35-p34.3 28348425 28375778 2 2 2
PTEN 5728 phosphatase and tensin homolog (mutated 10 10q23.3 89613175 89718512 10 9 9
in multiple advanced cancers 1)
PTGDR 5729 prostaglandin D2 receptor (DP) 14 14q22.1 51804181 51813192 13 13 13
PTGER3 5733 prostaglandin E receptor 3 (subtype EP3) 1 1p31.2 71090624 71286079 47 47 47
PTGER4 5734 prostaglandin E receptor 4 (subtype EP4) 5 5p13.1 40715789 40729594 7 6 6
PTGES 9536 prostaglandin E synthase 9 9q34.3 131540433 131555165 9 9 9
PTGIS 5740 prostaglandin I2 (prostacyclin) synthase 20 20q13.13 47553818 47618114 17 14 14
PTGS2 5743 prostaglandin-endoperoxide synthase 2 1 1q25.2-q25.3 184907592 184916179 8 7 6
(prostaglandin G/H synthase and
cyclooxygenase)
PTPNS1L 23755 protein tyrosine phosphatase, non- 22 22q12.2 29268342 29271028 4 4 4
receptor type substrate 1-like
PTPRA 5786 protein tyrosine phosphatase, receptor 20 20p13 2792841 2967315 19 19 19
type, A
PTX3 5806 pentraxin-related gene, rapidly induced 3 3q25 158637301 158644071 9 9 9
by IL-1 beta
RAC1 5879 ras-related C3 botulinum toxin substrate 1 7 7p22 6380651 6410123 20 18 18
(rho family, small GTP binding protein
Rac1)
REG3A 5068 regenerating islet-derived 3 alpha 2 2p12 79237641 79240387 3 2 2
REL 5966 v-rel reticuloendotheliosis viral oncogene 2 2p13-p12 60962256 61003682 7 6 6
homolog (avian)
RELA 5970 v-rel reticuloendotheliosis viral oncogene 11 11q13 65178393 65186951 5 5 5
homolog A, nuclear factor of kappa light
polypeptide gene enhancer in B-cells 3,
p65 (avian)
RELB 5971 v-rel reticuloendotheliosis viral oncogene 19 19q13.32 50196552 50233292 4 4 4
homolog B, nuclear factor of kappa light
polypeptide gene enhancer in B-cells 3
(avian)
RFXANK 8625 regulatory factor X-associated ankyrin- 19 19p12 19164008 19173678 5 4 4
containing protein
RHOB 388 ras homolog gene family, member B 2 2p24 20510316 20512682 6 6 6
RIPK1 8737 receptor (TNFRSF)-interacting serine- 6 6p25.2 3022057 3060420 10 9 9
threonine kinase 1
RIPK2 8767 receptor-interacting serine-threonine 8 8q21 90839110 90872433 9 8 8
kinase 2
RNASE7 84659 ribonuclease, RNase A family, 7 14 14q11.2 20580225 20582232 17 17 17
RPS6KA4 8986 ribosomal protein S6 kinase, 90 kDa, 11 11q11-q13 63883201 63896263 3 3 3
polypeptide 4
S100A12 6283 S100 calcium binding protein A12 1 1q21 151612808 151614699 5 5 5
S100A8 6279 S100 calcium binding protein A8 1 1q21 151629132 151630173 4 4 4
S100B 6285 S100 calcium binding protein B 21 21q22.3 46842959 46849463 12 11 11
SAA2 6289 serum amyloid A2 11 11p15.1-p14 18223365 18226744 13 12 12
SAA3P 6290 serum amyloid A3 pseudogene 11 11p15.1-p14 18090610 18094695 4 3 3
SAA4 6291 serum amyloid A4, constitutive 11 11p15.1-p14 18209479 18214910 12 11 11
SCUBE1 80274 signal peptide, CUB domain, EGF-like 1 22 22q13 41929174 42069299 85 83 83
SCYE1 9255 small inducible cytokine subfamily E, 4 4q24 107457124 107489021 5 4 4
member 1 (endothelial monocyte-
activating)
SELE 6401 selectin E (endothelial adhesion molecule 1 1q22-q25 167958406 167969803 18 18 18
1)
SELL 6402 selectin L (lymphocyte adhesion 1 1q23-q25 167926432 167947461 20 20 20
molecule 1)
SELP 6403 selectin P (granule membrane protein 1 1q22-q25 167824711 167866001 79 72 72
140 kDa, antigen CD62)
SELPLG 6404 selectin P ligand 12 12q24 107539800 107551799 12 10 10
SEMA7A 8482 semaphorin 7A, GPI membrane anchor 15 15q22.3-q23 72489376 72513329 14 14 14
(John Milton Hagen blood group)
SERPINA1 5265 serpin peptidase inhibitor, clade A (alpha- 14 14q32.1 93914451 93926782 26 25 25
1 antiproteinase, antitrypsin), member 1
SERPINA10 51156 serpin peptidase inhibitor, clade A (alpha- 14 14q32.13 93819403 93829349 23 23 23
1 antiproteinase, antitrypsin), member 10
SERPINA3 12 serpin peptidase inhibitor, clade A (alpha- 14 14q32.1 94148467 94160143 14 14 14
1 antiproteinase, antitrypsin), member 3
SERPINA5 5104 serpin peptidase inhibitor, clade A (alpha- 14 14q32.1 94117564 94129205 26 24 24
1 antiproteinase, antitrypsin), member 5
SERPINC1 462 serpin peptidase inhibitor, clade C 1 1q23-q25.1 172139565 172153096 16 14 14
(antithrombin), member 1
SERPIND1 3053 serpin peptidase inhibitor, clade D 22 22q11.2|22q11.21 19458383 19472008 6 6 6
(heparin cofactor), member 1
SERPINE1 5054 serpin peptidase inhibitor, clade E (nexin, 7 7q21.3-q22 100557172 100569026 19 19 19
plasminogen activator inhibitor type 1),
member 1
SERPINE2 5270 serpin peptidase inhibitor, clade E (nexin, 2 2q33-q35 224548118 224612237 20 20 20
plasminogen activator inhibitor type 1),
member 2
SERPINF2 5345 serpin peptidase inhibitor, clade F (alpha- 17 17p13 1592880 1605309 13 13 13
2 antiplasmin, pigment epithelium
derived factor), member 2
SERPING1 710 serpin peptidase inhibitor, clade G (C1 11 11q12-q13.1 57121603 57138902 8 8 8
inhibitor), member 1, (angioedema,
hereditary)
SFTPA1B 6435 surfactant, pulmonary-associated protein 10 81360664 81363921 4 4 4
A1B
SFTPA2B 6436 surfactant, pulmonary-associated protein 10 81305573 81310114 1 1 1
A2B
SFTPD 6441 surfactant, pulmonary-associated protein D 10 10q22.2-q23.1 81687476 81698841 16 16 16
SIGIRR 59307 single immunoglobulin and toll- 11 11p15.5 395716 407397 3 2 2
interleukin 1 receptor (TIR) domain
SIGLEC1 6614 sialic acid binding Ig-like lectin 1, 20 20p13 3615617 3635775 20 20 20
sialoadhesin
SLA2 84174 Src-like-adaptor 2 20 20q11.23 34674336 34707972 5 5 5
SOCS1 8651 suppressor of cytokine signaling 1 16 16p13.13 11255775 11257540 5 5 5
SOCS2 8835 suppressor of cytokine signaling 2 12 12q 92487729 92494109 5 5 5
SOCS3 9021 suppressor of cytokine signaling 3 17 17q25.3 73864454 73867753 5 5 5
SOCS4 122809 suppressor of cytokine signaling 4 14 14q22.1 54563594 54585960 3 3 3
SOCS5 9655 suppressor of cytokine signaling 5 2 2p21 46779603 46843431 14 14 14
SOCS6 9306 suppressor of cytokine signaling 6 18 18q22.2 66107117 66148414 14 14 14
SOD1 6647 superoxide dismutase 1, soluble 21 21q22.1|21q22.11 31953806 31963115 5 5 5
(amyotrophic lateral sclerosis 1 (adult))
SOD2 6648 superoxide dismutase 2, mitochondrial 6 6q25.3 160020138 160034343 7 7 7
SPACA3 124912 sperm acrosome associated 3 17 17q11.2 28342995 28349005 25 24 24
SPARC 6678 secreted protein, acidic, cysteine-rich 5 5q31.3-q32 151021201 151046710 17 17 17
(osteonectin)
SPINK4 27290 serine peptidase inhibitor, Kazal type 4 9 9p13.3 33230196 33238565 6 6 6
SPINK5 11005 serine peptidase inhibitor, Kazal type 5 5 5q32 147423759 147497120 16 15 15
SPN 6693 sialophorin (leukosialin, CD43) 16 16p11.2 29581801 29589329 3 3 3
SPP1 6696 secreted phosphoprotein 1 (osteopontin, 4 4q22.1 89115826 89123587 6 5 5
bone sialoprotein I, early T-lymphocyte
activation 1)
SRC 6714 v-src sarcoma (Schmidt-Ruppin A-2) 20 20q12-q13 35406502 35467235 15 15 15
viral oncogene homolog (avian)
SRF 6722 serum response factor (c-fos serum 6 6p21.1 43246898 43257222 6 6 6
response element-binding transcription
factor)
STAB1 23166 stabilin 1 3 3p21.1 52504396 52533551 12 11 11
STAT2 6773 signal transducer and activator of 12 12q13.3 55021648 55040176 3 3 3
transcription 2, 113 kDa
STAT3 6774 signal transducer and activator of 17 17q21.31 37718869 37794039 11 11 11
transcription 3 (acute-phase response
factor)
STAT4 6775 signal transducer and activator of 2 2q32.2-q32.3 191602551 191724170 40 39 39
transcription 4
STAT5A 6776 signal transducer and activator of 17 17q11.2 37693091 37717484 3 3 3
transcription 5A
STAT5B 6777 signal transducer and activator of 17 17q11.2 37604721 37681950 4 4 4
transcription 5B
STAT6 6778 signal transducer and activator of 12 12q13 55775458 55791428 10 8 8
transcription 6, interleukin-4 induced
STX4 6810 syntaxin 4 16 16p11.2 30952404 30958986 1 1 1
SYK 6850 spleen tyrosine kinase 9 9q22 92603891 92698305 71 69 69
TACR1 6869 tachykinin receptor 1 2 2p12 75129738 75279781 50 49 49
TANK 10010 TRAF family member-associated NFKB 2 2q24-q31 161701712 161800928 10 9 9
activator
TBK1 29110 TANK-binding kinase 1 12 12q14.1 63132204 63182158 5 5 5
TBX21 30009 T-box 21 17 17q21.32 43165609 43178484 7 6 6
TBXA2R 6915 thromboxane A2 receptor 19 19p13.3 3545504 3557658 13 10 10
TBXAS1 6916 thromboxane A synthase 1 (platelet, 7 7q34-q35 139175421 139366471 59 59 59
cytochrome P450, family 5, subfamily A)
TEK 7010 TEK tyrosine kinase, endothelial (venous 9 9p21 27099286 27220172 81 81 81
malformations, multiple cutaneous and
mucosal)
TFPI 7035 tissue factor pathway inhibitor 2 2q32 188037202 188127464 42 37 37
(lipoprotein-associated coagulation
inhibitor)
TGFB1 7040 transforming growth factor, beta 1 19 19q13.2|19q13.1 46528491 46551656 10 10 10
TGFB2 7042 transforming growth factor, beta 2 1 1q41 216586491 216681596 26 25 25
TGFB3 7043 transforming growth factor, beta 3 14 14q24 75494195 75517242 8 8 8
TGFBR1 7046 transforming growth factor, beta receptor 9 9q22 100907233 100956295 7 7 7
I (activin A receptor type II-like kinase,
53 kDa)
TGFBR2 7048 transforming growth factor, beta receptor 3 3p22 30622998 30710638 42 41 41
II (70/80 kDa)
THBD 7056 thrombomodulin 20 20p11.2 22974270 22978301 16 14 14
THBS1 7057 thrombospondin 1 15 15q15 37660572 37676960 22 22 22
THBS4 7060 thrombospondin 4 5 5q13 79366747 79414866 16 15 15
TICAM1 148022 toll-like receptor adaptor molecule 1 19 19p13.3 4766992 4769451 4 3 3
TIMP1 7076 TIMP metallopeptidase inhibitor 1 X Xp11.3-p11.23 47326634 47331134 3 3 3
TIRAP 114609 toll-interleukin 1 receptor (TIR) domain 11 11q24.2 125658192 125670038 14 13 13
containing adaptor protein
TLR1 7096 toll-like receptor 1 4 4p14 38474271 38482807 7 5 5
TLR10 81793 toll-like receptor 10 4 4p14 38450629 38460984 16 13 13
TLR2 7097 toll-like receptor 2 4 4q32 154824891 154846693 12 9 9
TLR3 7098 toll-like receptor 3 4 4q35 187227303 187243246 10 10 10
TLR4 7099 toll-like receptor 4 9 9q33.1 119506431 119519589 14 13 13
TLR5 7100 toll-like receptor 5 1 1q41-q42 221350207 221383247 10 9 9
TLR6 10333 toll-like receptor 6 4 4p14 38504803 38507555 6 5 5
TLR7 51284 toll-like receptor 7 X Xp22.3 12795123 12818401 18 16 16
TLR8 51311 toll-like receptor 8 X Xp22 12834679 12851209 15 13 13
TLR9 54106 toll-like receptor 9 3 3p21.3 52230138 52235219 6 4 4
TMED7 51014 transmembrane emp24 protein transport 5 5q22.3 114977102 114989595 7 7 7
domain containing 7
TNF 7124 tumor necrosis factor (TNF superfamily, 6 6p21.3 31651329 31654091 19 15 15
member 2)
TNFAIP3 7128 tumor necrosis factor, alpha-induced 6 6q23 138230274 138246142 6 6 6
protein 3
TNFAIP8 25816 tumor necrosis factor, alpha-induced 5 5q23.1 118632317 118758193 6 6 6
protein 8
TNFRSF10A 8797 tumor necrosis factor receptor 8 8p21 23104915 23138584 19 18 18
superfamily, member 10a
TNFRSF10C 8794 tumor necrosis factor receptor 8 8p22-p21 23016379 23030895 11 9 9
superfamily, member 10c, decoy without
an intracellular domain
TNFRSF1A 7132 tumor necrosis factor receptor 12 12p13.2 6308184 6321522 10 9 9
superfamily, member 1A
TNFRSF1B 7133 tumor necrosis factor receptor 1 1p36.22 12149647 12191864 26 24 24
superfamily, member 1B
TNFRSF21 27242 tumor necrosis factor receptor 6 6p21.1 47307227 47385639 28 26 26
superfamily, member 21
TNFRSF25 8718 tumor necrosis factor receptor 1 1p36.2 6443798 6448842 6 5 5
superfamily, member 25
TNFRSF8 943 tumor necrosis factor receptor 1 1p36 12046021 12126851 27 27 27
superfamily, member 8
TNFRSF9 3604 tumor necrosis factor receptor 1 1p36 7902494 7923474 5 5 5
superfamily, member 9
TNFSF15 9966 tumor necrosis factor (ligand) 9 9q32 116591421 116608229 8 8 8
superfamily, member 15
TNIP1 10318 TNFAIP3 interacting protein 1 5 5q32-q33.1 150389699 150441190 31 29 29
TOLLIP 54472 toll interacting protein 11 11p15.5 1252177 1287415 10 10 10
TP53 7157 tumor protein p53 17 17p13.1 7512445 7531642 5 5 5
TPST1 8460 tyrosylprotein sulfotransferase 1 7 7q11.21 65307750 65462865 8 8 8
TRADD 8717 TNFRSF1A-associated via death domain 16 16q22 65745589 65751313 3 1 1
TRAF1 7185 TNF receptor-associated factor 1 9 9q33-q34 122704493 122728994 6 6 6
TRAF2 7186 TNF receptor-associated factor 2 9 9q34 138900786 138940888 14 14 14
TRAF3 7187 TNF receptor-associated factor 3 14 14q32.32 102313569 102442381 16 16 16
TRAF5 7188 TNF receptor-associated factor 5 1 1q32 209566580 209614911 6 6 6
TRAF6 7189 TNF receptor-associated factor 6 11 11p12 36467302 36488398 11 11 11
TREM1 54210 triggering receptor expressed on myeloid 6 6p21.1 41351690 41362435 11 10 10
cells 1
TTN 7273 titin 2 2q31 179098962 179380395 36 36 36
TXN 7295 thioredoxin 9 9q31 112046131 112058599 23 23 23
TYK2 7297 tyrosine kinase 2 19 19p13.2 10322209 10352211 11 9 9
TYMP 1890 thymidine phosphorylase 22 22q13|22q13.33 49311047 49315321 8 8 8
UBE2D3 7323 ubiquitin-conjugating enzyme E2D 3 4 4q24 103936217 104009473 10 10 10
(UBC4/5 homolog, yeast)
UBTF 7343 upstream binding transcription factor, 17 17q21.3 39637927 39653776 3 3 3
RNA polymerase I
USF1 7391 upstream transcription factor 1 1 1q22-q23 159275665 159282381 9 9 9
VASP 7408 vasodilator-stimulated phosphoprotein 19 19q13.2-q13.3 50702528 50722081 11 11 11
VCAM1 7412 vascular cell adhesion molecule 1 1 1p32-p31 100957885 100977189 13 13 13
VCL 7414 vinculin 10 10q22.2 75427878 75549924 14 12 12
VEGFA 7422 vascular endothelial growth factor A 6 6p12 43845931 43862202 15 15 15
VEGFB 7423 vascular endothelial growth factor B 11 11q13 63758842 63762835 5 4 4
VEGFC 7424 vascular endothelial growth factor C 4 4q34.3 177841685 177950889 11 11 11
VISA 57506 virus-induced signaling adapter 20 20p13 3775484 3795973 9 9 9
VKORC1 79001 vitamin K epoxide reductase complex, 16 16p11.2 31009676 31013777 2 2 2
subunit 1
VPS45 11311 vacuolar protein sorting 45 homolog (S. cerevisiae) 1 1q21.2 148305966 148384129 4 4 4
VTN 7448 vitronectin 17 17q11 23718425 23721500 6 5 5
VWF 7450 von Willebrand factor 12 12p13.3 5928301 6104097 155 148 148
XCL1 6375 chemokine (C motif) ligand 1 1 1q23 166812480 166817939 8 8 8
XCR1 2829 chemokine (C motif) receptor 1 3 3p21.3-p21.1| 46037295 46043983 4 3 3
3p21.3
YARS 8565 tyrosyl-tRNA synthetase 1 1p35.1 33013427 33056220 7 7 7
YY1 7528 YY1 transcription factor 14 14q 99774855 99814557 4 4 4
12283 12226
Genotyping and Quality Control Leukocyte genomic DNA was extracted, quantified, and diluted to the appropriate concentration for Illumina Infinium iSelect genotyping on all samples collected. Controls included 2% sample replicates and a CEPH trio for quality control. In addition, case and control DNA sample addresses were randomly assigned across both the 96-well plate as well as the 12-address iSelect BeadChip, insuring approximately equal numbers of case and control DNA samples by each strata to avoid potential plate and chip effects, respectively. Genotyping results from high-quality control DNA (SNP call rate 95%) was used to generate a cluster algorithm.
Statistical Analyses The primary outcome was VTE status, a binary measure. The covariates were age at interview or blood sample collection, sex, stroke and/or MI status, and state of residence (Table 2). To adjust for population stratification, the multidimensional scaling (MDS) analysis option in PLINK v 1.07 was performed to identify outliers in the population (Purcell et al., American Journal of Human Genetics., 81:559-75 (2007)) using the ancestry informative markers. Association between each SNP and VTE were tested for using unconditional logistic regression, adjusting for age, sex, stroke/MI status, and state of residence. The analyses were corrected for multiple comparisons using an extension of false discovery rates (Benjamini et al., Behavioural Brain Research., 125:279-84 (2001) and Storey et al., Proc. Nat'l. Acad. Sci. USA, 100:9440-5 (2003)). The false discovery rate was an analogue measure of the p-value that takes into account the number of statistical tests and estimates the expected proportion of false positive tests incurred when a particular SNP is significant. All analyses were performed using PLINK v 1.07 Purcell et al., American Journal of Human Genetics., 81:559-75 (2007)). Quantile-quantile (QQ) plots of observed −log10 p-values for VTE association versus the expected −log10 p-values under the null hypothesis of no association were generated to display the potential significant associations (Wakefield, International Journal of Epidemiology, 37:641-53 (2008), and to calculate the genomic inflation factor as a check for over dispersion of the test statistics (Clayton et al., Nature Genetics, 37:1243-6 (2005). Penalized logistic regression models were used to determine possible interaction between the statistically significant SNPs (Park and Hastie, Biostatistics, 9:30-50 (2008)).
TABLE 2
Demographic and Clinical Characteristics by Case-Control Status
Case Control
Characteristic n = 1488 n = 1439 P-value
Patient age, mean ± SD, years 54.7 ± 16.3 55.5 ± 15.7 0.1796
Female, n (%) 751 (50.5) 754 (52.4) 0.2970
Stroke or myocardial 283 (19.0) 149 (10.4) <0.0001
infarction, n (%)
State of residence, n (%) <0.0001
Minnesota 619 (41.6) 795 (55.2)
Other States 869 (58.4) 644 (44.8)
Population attributable risk (PAR) was estimated for each genotype, which defines the percentage of the total risk for VTE due to genetic effect of that particular genotype (Cole and MacMahon, British Journal of Preventive & Social Medicine, 25:242-4 (1971):
where p is the prevalence of risk genotype associated with VTE among control subjects, and OR is the odds ratio associated with risk genotype. Odds ratios from the dominant genetic model adjusted for age at blood draw, gender, MI/stroke status, and state of residence were used. The group PAR was calculated as:
on the basis of the individual PARi of each associated genotype assuming a dominant genetic model and no multiplicative interaction among the genotypes (i.e., assuming independence between SNPs). The joint PAR was calculated as:
assuming multiple loci, ρ1 as the fraction of cases for each associated genotype, and ORj as the individual OR for each associated SNP or genotype calculated under the full logistic regression model (Bruzzi et al., American Journal of Epidemiology, 122:904-14 (1985)). The PAR was calculated, both unadjusted and adjusted, assuming a dominant genetic model for the genotypes. The AttribRisk Splus function (glm function, binomial error) was used to estimate this PAR, unadjusted and adjusted for covariates using jackknife estimates for the standard error (Kahn et al., Technical Report Series No 54 Department of Health Science Research, Mayo Clinic Rochester, Minn., 1994).
Results Of the 3131 unique subjects recruited, 204 were excluded due to the following overlapping reasons: study exclusion criteria (n=78), genotype issues (n=40; 22 failed genotyping and 18 had a genotype call rate <95%), mislabeled samples (n=32), and non-European (i.e., African- or Asian-American) race (n=20). Thirty-four subjects were removed due to relatedness using IBS clustering in PLINK. Multidimensional scaling plots showed two subjects with race discrepancy (FIG. 10). After removal of these subjects, no evidence of population stratification was found. After these exclusions, a total of 2,927 individuals (1,488 VTE subjects [51%], 1,439 controls; 51% women) were included in the analyses. The study population demographic and clinical characteristics by case status are presented in Table 2. Among the cases, the distribution of symptomatic VTE by event type was DVT only (n=744; 50%), PE only (n=390; 26.2%), and both DVT and PE (n=354; 23.8%).
Of the 14,612 SNPs submitted to Illumina from 764 genes within the anticoagulant, procoagulant, fibrinolytic and innate immunity pathways (Table 3), 1,585 SNPs (covering 1,100 LD bins) failed manufacture. Of the remaining 13,027 successfully manufactured SNPs (Illumina) and 4 SNPs on TaqMan, 735 SNPs were excluded due to poor performance (n=554), a MAF <0.005 (n=127) or a call rate <0.95 (n=54), leaving 12,296 SNPs (covering 10,456 bins) for the association analysis. Prior to exclusion, concordance between the genotype results for Factor V Leiden (F5 rs6025) and data obtained clinically for cases was 100% (218/218) between positive cases and 99% (446/450) between negative cases.
TABLE 3
Number of LD Bins after Illumina Infinium Custom Genotyping SNP
Selection, Design, Manufacture and Assay by Pathway
Pathway After After After After % Total
(# of Genes)* Selection Design Manufacture QC Lost
Anticoagulant (16) 234 232 214 210 10.3
Procoagulant (75) 1516 1466 1354 1300 14.2
Fibrinolytic (23) 435 411 373 356 18.2
Innate 10373 9964 9032 8590 17.2
Immunity (635)
*15 genes out of 764 did not have SNPs after quality control (QC)
Using an additive genetic model and adjusting for age, gender, stroke/MI status and state of residence, and a false discovery rate (q-value)<0.05, one or more SNPs within ABO, F2, F5, F11, KLKB1, SELP and SCUBE1 were significantly associated with VTE (Table 4 and FIG. 11). The association between VTE and Factor V Leiden (F5 rs6025, OR=3.40, p-value=3.07×10−22) was confirmed, but after controlling for F5 rs6025, F5 rs6687813 was not associated with VTE. The association between VTE and ABO non-O blood type (ABO rs8176719, OR=1.47, p-value=5.68×10−12) was also confirmed, and a novel association with ABO rs2519093 (OR=1.69, p-value=8.08×10−16) that remained significant after controlling for non-O blood type (OR=1.52, p-value=1.35×10−6; FIG. 12) was found. An association between VTE and prothrombin G20210A (F2 rs1799963, OR=2.46, p-value=1.69×10−6) was found. An association analysis using a dominant genetic model gave similar results.
TABLE 4
Association* of Candidate Gene SNPs with Venous Thromboembolism.
Minor Odds
SNP Gene Chromosome Allele N Ratio P-value Q-value
rs6025 F5 1 A 2927 3.40 3.07E−22 3.77E−18
rs6687813 F5 1 A 2926 2.13 4.66E−16 2.86E−12
rs2519093 ABO 9 A 2907 1.68 8.08E−16 3.31E−12
rs505922 ABO 9 G 2926 1.49 1.52E−12 4.68E−09
rs687289 ABO 9 A 2924 1.48 3.03E−12 7.46E−09
rs8176719 ABO 9 G 2900 1.47 5.68E−12 1.16E−08
rs643434 ABO 9 A 2923 1.44 3.39E−11 5.96E−08
rs630014 ABO 9 A 2927 0.75 2.67E−07 0.00041
rs3087505† KLKB1 4 A 2927 0.63 4.34E−07 0.000593
rs660340 ABO 9 A 2927 0.77 1.13E−06 0.001389
rs659104 ABO 9 A 2927 0.77 1.28E−06 0.001425
rs1799963 F2 11 A 2891 2.46 1.69E−06 0.001732
rs3917862 SELP 1 G 2924 1.60 6.13E−06 0.005562
rs4253399‡ F11 4 C 2927 1.28 6.33E−06 0.005562
rs4525 F5 1 G 2924 0.77 2.34E−05 0.01917
rs4524 F5 1 G 2927 0.77 2.51E−05 0.01932
rs10158595 F5 1 A 2927 0.76 3.03E−05 0.02191
rs6032 F5 1 G 2916 0.77 3.35E−05 0.02253
rs5759224 SCUBE1 22 G 2864 1.43 3.48E−05 0.02253
rs2213867 F5 1 G 2926 0.78 4.37E−05 0.02685
*Additive model; adjusted for age, gender, stroke/myocardial infarction and state of residence.
†SNP within 10 kb of F11
‡SNP within 10 kb of KLKB1
Four additional analyses stratifying by sex, Factor V Leiden (positive/negative for carrier of F5 rs6025 A allele), ABO blood type-O (yes/no based on homozygous deletion in ABO rs8176719 where the homozygous deletion results in ABO blood type-O) and prothrombin G20210A (positive/negative for carrier of F2 rs1799963 A allele) were performed. Similar F5 and ABO SNPs were associated with VTE for both females and males, while F2 rs1799963 was no longer significant for either gender; SNPs within an additional gene (LY86) was significantly associated with VTE among females (Table 5). The odds of VTE appeared to be higher for Factor V Leiden among males. Among Factor V Leiden non carriers, similar ABO and F2 SNPs, and an additional KLKB1 SNP were associated with VTE (Table 6). Among Factor V Leiden carriers, SNPs within PRKCB1 and CD44 were marginally associated with VTE, possibly due to small sample size. Among persons with ABO blood type non-O (ABO rs8176719 G), SNPs within F5, F11 and KLKB1, and an additional gene (GFRA1) were associated with VTE (Table 7). Of note, the ABO rs2519093 remained significantly associated with VTE in this patient subset. Only the Factor V Leiden mutation was significantly associated with VTE among those with the ABO blood type-O (ABO rs8176719 G homozygous deletion). Among prothrombin G20210A non-carriers, SNPs within ABO, F5, F11, KLKB1, SCUBE1 and SELP were significantly associated with VTE (Table 5). The sample size of prothrombin G20210A carriers was insufficient for meaningful analysis. Sex-chromosome analysis was also performed, and no significant results were identified. Q-Q plots of the −log10 p-values for SNP associated with VTE under different analyses showed no evidence of over dispersion in the samples (λ=1.0; FIG. 13).
TABLE 5
Association* of Candidate Gene SNPs with
Venous Thromboembolism Stratified by Sex.
Minor Odds
SNP Gene Chromosome Allele N Ratio P-value Q-value
Females
rs6025 F5 1 A 1505 2.80 8.38E−10 1.03E−05
rs6687813 F5 1 A 1504 2.04 4.71E−08 0.000289
rs8176719 ABO 9 G 1487 1.51 1.38E−07 0.000332
rs643434 ABO 9 A 1503 1.51 1.45E−07 0.000332
rs687289 ABO 9 A 1503 1.51 1.52E−07 0.000332
rs505922 ABO 9 G 1505 1.51 1.62E−07 0.000332
rs2519093 ABO 9 A 1496 1.58 2.21E−07 0.000388
rs1073897 LY86 6 A 1496 0.68 6.41E−06 0.009845
rs630014 ABO 9 A 1505 0.71 1.26E−05 0.01728
rs9328375 LY86 6 A 1504 0.71 2.97E−05 0.03656
Males
rs6025 F5 1 A 1422 4.28 7.37E−14 9.06E−10
rs2519093 ABO 9 A 1411 1.82 3.46E−10 2.13E−06
rs6687813 F5 1 A 1422 2.20 3.98E−09 1.63E−05
rs505922 ABO 9 G 1421 1.48 1.26E−06 0.003881
rs687289 ABO 9 A 1421 1.46 2.55E−06 0.006264
rs8176719 ABO 9 G 1413 1.44 5.11E−06 0.01046
rs643434 ABO 9 G 1421 1.39 2.7E−05 0.04738
*Additive model; adjusted for age, stroke/myocardial infarction and state of residence.
TABLE 6
Association* of Candidate Gene SNPs with Venous
Thromboembolism Stratified by Factor V Leiden.
Minor Odds
SNP Gene Chromosome Allele N Ratio P-value Q-value
Factor V Leiden non-carrier (F5 rs6025 G)
rs2519093 ABO 9 A 2543 1.67 1.06E−13 1.3E−09
rs505922 ABO 9 G 2557 1.46 2.33E−10 1.43E−06
rs687289 ABO 9 A 2555 1.45 5.27E−10 2.16E−06
rs8176719 ABO 9 G 2535 1.44 7.71E−10 2.37E−06
rs643434 ABO 9 A 2555 1.41 6.61E−09 1.62E−05
rs630014 ABO 9 A 2558 0.74 3.76E−07 0.00077
rs3087505† KLKB1 4 A 2558 0.61 7.35E−07 0.00129
rs1799963 F2 11 A 2528 2.63 9.5E−07 0.00146
Factor V Leiden carrier (F5 rs6025 A)
rs195999 PRKCB1 16 C 368 0.49 2.87E−05 0.1778
rs7404320 PRKCB1 16 G 369 0.49 2.89E−05 0.1778
rs11033021 CD44 11 A 365 2.27 7.42E−05 0.2176
rs196002 PRKCB1 16 A 369 0.51 7.44E−05 0.2176
rs8044722 PRKCB1 16 A 369 0.50 8.85E−05 0.2176
rs7945310 CD44 11 A 369 0.46 0.000127 0.2287
rs9924860 PRKCB1 16 C 369 1.98 0.00013 0.2287
rs2188355 PRKCB1 16 A 368 0.52 0.000188 0.2887
rs12931116 PRKCB1 16 G 368 1.92 0.000246 0.3072
rs11130068 ITPR1 3 G 369 0.44 0.00025 0.3072
*Additive model; adjusted for age, gender, stroke/myocardial infarction and state of residence.
†SNP is on KLKB1 gene but within 10 kb of F11
TABLE 7
Association* of Candidate Gene SNPs with Venous Thromboembolism
Stratified by ABO non-O Blood Type (ABO rs8170719 [G]).
Minor Odds
SNP Gene Chromosome Allele N Ratio P-value Q-value
ABO blood type non-O (ABO rs8170719 G)
rs6025 F5 1 A 1965 3.79 1.46E−16 1.79E−12
rs6687813 F5 1 A 1965 2.47 3.76E−14 2.31E−10
rs2519093 ABO 9 A 1945 1.43 4.2E−06 0.01723
rs3087505† KLKB1 4 A 1965 0.59 7.59E−06 0.01873
rs1799963 F2 11 A 1933 3.09 7.62E−06 0.01873
rs10749203 GFRA1 10 A 1959 0.72 1.08E−05 0.02101
rs8176704 ABO 9 A 1965 0.62 1.2E−05 0.02101
rs4253399‡ F11 4 C 1965 1.34 1.83E−05 0.02816
rs881726 GFRA1 10 G 1965 0.72 3.04E−05 0.04157
rs10787637 GFRA1 10 G 1964 0.74 3.86E−05 0.04743
ABO blood type-O (ABO rs8170719 G homozygous deletion)
rs6025 F5 1 A 962 2.72 2.18E−06 0.02675
*Additive model; adjusted for age, gender, stroke/myocardial infarction and state of residence.
†SNP is on KLKB1 gene but within 10 kb of F11
‡SNP is on F11 gene but within 10 kb of KLKB1
TABLE 8
Association* of Candidate Gene SNPs with Venous Thromboembolism
among Prothrombin G20210A (F2 rs1799963 A) Non-Carriers.
Minor Odds
SNP Gene Chromosome Allele N Ratio P-value Q-value
rs6025 F5 1 A 2787 3.49 2.91E−22 3.58E−18
rs6687813 F5 1 A 2786 2.20 1.46E−16 8.98E−13
rs2519093 ABO 9 A 2767 1.65 3.24E−14 1.33E−10
rs505922 ABO 9 G 2786 1.48 9.06E−12 2.79E−08
rs687289 ABO 9 A 2786 1.47 1.39E−11 3.42E−08
rs8176719 ABO 9 G 2760 1.46 2.39E−11 4.9E−08
rs643434 ABO 9 A 2784 1.44 9.85E−11 1.73E−07
rs630014 ABO 9 A 2787 0.75 3.41E−07 0.000524
rs3087505† KLKB1 4 A 2787 0.62 5.75E−07 0.000786
rs660340 ABO 9 A 2787 0.77 2.68E−06 0.0033
rs659104 ABO 9 A 2787 0.77 3.03E−06 0.003388
rs4253399‡ F11 4 C 2787 1.28 9.03E−06 0.009256
rs3917862 SELP 1 G 2784 1.60 1.28E−05 0.01214
rs5759224 SCUBE1 22 G 2730 1.46 1.95E−05 0.01713
rs4525 F5 1 G 2784 0.76 2.13E−05 0.01743
rs4524 F5 1 G 2787 0.76 2.3E−05 0.01751
rs10158595 F5 1 A 2787 0.76 2.42E−05 0.01751
rs6032 F5 1 G 2777 0.76 2.86E−05 0.01951
rs2213867 F5 1 G 2784 0.77 4.02E−05 0.02604
*Additive model; adjusted for age, gender, stroke/myocardial infarction and state of residence.
†SNP is on KLKB1 gene but within 10 kb of F11
‡SNP is on F11 gene but within 10 kb of KLKB1
The individual, joint, and group population attributable risk (PAR) were calculated for the risk genotypes for Factor V Leiden (F5 rs6025), prothrombin G20210A (F2 rs1799963), ABO blood type non-O (ABO rs8176719), as well as the novel ABO rs2519093 (Table 9). The unadjusted and adjusted individual and joint PARs values were very similar. The highest PAR value was from the ABO blood type non-O, followed by ABO rs2519093, Factor V Leiden, and prothrombin G20210A. The PAR values were very similar between the joint and group estimation methods when either ABO rs8176719 or ABO rs2519093 was included. When both ABO rs8176719 and ABO rs2519093 were included in the group PAR calculation, the method yielded an inflated value of 0.59 compared to the joint method (joint PAR=0.45).
TABLE 9
Attributable Risk (AR) for Significant Single Nucleotide
Polymorphisms (SNPs) Assuming A Dominant Genetic
Model for Each SNP.
Single Nucleotide Unadjusted Adjusted†
Polymorphism AR 95% CI AR 95% CI
Individual
F5 rs6025 0.13 (0.10, 0.16) 0.14 (0.11, 0.16)
(Factor V Leiden)
F2 rs1799963 (Prothrombin 0.04 (0.02, 0.06) 0.04 (0.02, 0.06)
G20210A)
ABO rs8176719 (ABO 0.35 (0.27, 0.42) 0.35 (0.24, 0.47)
blood type non-O)
ABO rs2519093 0.25 (0.19, 0.33) 0.25 (0.17, 0.32)
Joint*
F5 rs6025, F2 rs1799963, 0.45 (0.36, 0.54) 0.45 (0.37, 0.54)
ABO rs8176719
F5 rs6025, F2 rs1799963, 0.36 (0.30, 0.42) 0.36 (0.30, 0.42)
ABO rs2519093
F5 rs6025, F2 rs1799963, 0.45 (0.36, 0.54) 0.45 (0.36, 0.53)
ABO rs8176719,
ABO rs2519093
Group‡
F5 rs6025, F2 rs1799963, — 0.46 —
ABO rs8176719
F5 rs6025, F2 rs1799963, — 0.39 —
ABO rs2519093
F5 rs6025, F2 rs1799963, — 0.59 —
ABO rs8176719,
ABO rs2519093
*Bruzzi et al., American Journal of Epidemiology, 122: 904-14 (1985).
†Adjusted for age at blood sample collection, male gender, myocardial infarction/stroke status, and Minnesota residence.
‡Assuming independence between SNPs, i.e., a non-multiplicative interaction between the genotypes.
The results provided herein demonstrate that an association exists between Factor V Leiden, prothrombin G20210A and VTE as well as between ABO blood type non-O and VTE. These results also demonstrate that an ABO intron 1 tag SNP is strongly and independently associated with VTE. Together, these SNPs account for 45% of VTE within this population.
In addition, the results provided herein identified additional SNPs within KLKB1, F11, SELP, SCUBE1, and LY86 that also appear to be strongly associated with VTE. These findings lend further support to the hypothesis that individual genetic variation in genes encoding for components of the procoagulant, anticoagulant, fibrinolytic, and innate immunity pathways predispose to incident VTE.
Example 3 A Genome-Wide Association Study of Venous Thromboembolism Identifies Risk Variants in Chromosomes 1q24.2 and 9q Genotyping Candidate Gene Leukocyte genomic DNA was extracted, quantified, and diluted to the appropriate concentration for Illumina Infinium iSelect genotyping on all samples collected as described in Example 2. Controls included 2% sample replicates and a CEPH trio for quality control at the Mayo Clinic Technology Center. In addition, case and control DNA sample addresses were randomly assigned across both the 96-well plate as well as the 12-address iSelect BeadChip, insuring approximately equal numbers of case and control DNA samples by each strata to avoid potential plate and chip effects, respectively. Genotyping results from high-quality control DNA (SNP call rate 95%) was used to generate a cluster algorithm. Of the 14,612 SNPs submitted to Illumina from 764 genes within the anticoagulant, procoagulant, fibrinolytic, and innate immunity pathways, 1,585 SNPs (covering 1,100 LD bins) failed manufacture, leaving 13,027 SNPs for analysis.
GWA The Center for Inherited Disease Research (CIDR), one of the two genotyping centers supported by the GENEVA consortium (Cornelius et al., Genet. Epidemiol., published online, doi: 10.1002/gepi.20492 (20 Jan. 2010)), genotyped samples using the Illumina Human610-Quad v. 1_B BeadChip (Illumina). The DNA source for all samples came from whole blood. Case and control DNA sample addresses were randomly assigned across 96-well plates provided by CIDR while assuring roughly equal percentages of cases and controls within each plate. Genotype clusters for each SNP were determined using the IlluminaBeadStudio Module (version 3.3.7), and combined intensity data from 99.2% of samples were used to define clusters and call genotypes. Overall, 99.1% of samples attempted (7,114 of 7,178 total) passed quality-control standards. Genotypes were not called if the quality score from BeadStudio was <0.15. Both the mean SNP call rates and the mean sample call rates were 99.8%. Genotypes were released for 589,945 SNPs (99.56% of those attempted). Genotypes were not released for autosomal SNPs with call rates <85%, >1 HapMap replicate error, >1% difference in call rate between genders or >4% difference in heterozygote frequency. Duplicate samples from both HapMap and the study were included on each plate. Reproducibility rates in the raw data were 99.99% among 161 duplicated subjects. Samples included 169 blind duplicates, and 98.8% of these duplicates met quality-control criteria. CIDR's release criteria depended on sample source: samples with >96.5% called genotypes were released for DNA from whole blood.
Quality-Control Steps For both CG and GWA, four main categories of quality-control flags were set for autosomal SNPs: (i) unacceptably high rates of missing genotype calls, (ii) low MAF, (iii) unacceptably high rates of Mendelian errors, and (iv) deviation from Hardy-Weinberg equilibrium (HWE).
For the GWA study, 1,965 SNPs with >5% missing genotypes were flagged. A total of 1,683/1,115/1,135 SNPs were flagged overall/cases/controls for HWE deviation at P<10 −5. For the CG study, 735 SNPs were excluded due to poor performance (n=554), a MAF<0.005 (n=127), or a call rate <0.95 (n=54), leaving 12,296 SNPs (covering 10,456 bins) for the association analysis.
Population Stratification To test for “cryptic relatedness” in the population, a population structure analysis was conducted on all participating subjects to document genetic diversity among the population. Using 494 Ancestry Informative Markers (AIMS) available on both the candidate gene and the GWA studies (Seldin et al., PLoS Genetics, 2:e143 (2006)), STRUCTURE was run on 2962 participants (Pritchard et al., Genetics, 155:945-959 (2000)). The triangle plot provided a graphical representation of genetic structure of the participants plus 209 unrelated individuals from HapMap phase II populations (Yorubans [YRI]; European-Americans from the CEPH collection [CEU]; Chinese from Beijing [CHB]; and Japanese from Tokyo [JPT]), giving a clear sense of how the participants fall among the HapMap reference populations (FIG. 14).
Imputation MACH was used for imputation of genotypes to the HapMap phase II CEU reference set of approximately 2.5 million SNPs. All genetic coordinates in tables and figures for this example refer to HapMap release 22 build 36. In regions where no candidate gene genotypes were available, only subjects with GWA data were used for the imputation.
Replication Samples Seven SNPs chosen for replication were genotyped in a total of 2,883 individuals (VTE cases, n=1451; controls, n=1432). Replication leukocyte genomic DNA samples were largely from Olmsted County, Minn., USA residents with objectively-diagnosed incident VTE over the 45-year period, and previously-matched Olmsted County resident controls as described elsewhere (Heit et al., Arch. Intern. Med., 160:809-815 (2000); Heit et al., J. Thromb. Haemost., 3:710-17 (2005); and Heit et al., Arterioscler. Thromb. Vasc. Biol., 29:1399-1405 (2009)). The replication case and control sample size was augmented by leukocyte DNA from non-Olmsted County Mayo Clinic patients identified as described for the CG study population for Example 2.
DNA Sequencing Sixteen genes were selected for deep sequencing in 84 VTE cases and 12 controls, including 5 genes harboring SNPs significantly associated with VTE (F5, SLC19A2, ABO, NME7, and ATP1B1), 10 genes with SNPs marginally associated with VTE (Clorf114, KLKB1, SELP F11, SCUBE1, PRKCB1, CD44, ITPR1, GFRA1, and BLZF1), and CYP4V2 which reportedly confounds F11 and KLKB1. Agilent SureSelect probes were designed to capture and enrich the Mb genomic regions of these 16 genes. Samples were multiplexed (12-plex) and sequenced using Illumina HiSeq 2000. The sequence reads were aligned to the human genome build 36 using Burrows-Wheeler Aligner, and the single nucleotide variants (SNVs) and small INDELs were called using SNVMix and GATK, respectively.
Capture of the target genomic regions was performed using the Agilent custom eArray. The capturing probes (baits) of 120 bases in length were designed based on the paired-end sequencing protocol with a tiling frequency of 3×. The standard repeat masked regions were avoided based on the definition in the UCSC genome database. The repeat regions were mostly in intronic regions of the genes.
Sequencing was performed using Illumina's HiSeq 2000 sequencer. Twelve samples were multiplexed in each lane of the 8-lane flow cell, and a total of 96 samples (84 VTE cases and 12 controls) were sequenced. The read qualities were examined by FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc), which generates QC matrix from the FASTQ files including per-base sequence qualities, per-sequence quality scores, per-base nucleotide content, and sequence duplication levels. The FastQC tool also provided warnings for parameters failing to pass QC thresholds. The paired-end 100-base reads were aligned to human genome build 36 using BWA (Li et al., Annu. Rev. Genomics Hum. Genet., 10:387-406 (2009)), allowing 4% of mismatches with a seed length of 32. If the sequence duplication levels failed to pass the FastQC threshold, the duplicated reads were removed using the SAMtools's rmdup method (Li et al., Annu. Rev. Genomics Hum. Genet., 10:387-406 (2009)). The BWA alignment was then cleaned up and improved using the Genome Analysis ToolKit (GATK) local re-alignments. SNVs were called using SNVMix with a cut-off probability score of 0.8 based on preliminary testing using a HapMap CEPH subject sequenced by the 1000 genome project (data not shown), and INDELs were called by GATK with default parameters setting.
The read depths of each of the A, C, G, T bases at each variant position, as well as the average mapping quality score were provided by curating the BAM pile-up files using SAMtools (Li et al., Annu. Rev. Genomics Hum. Genet., 10:387-406 (2009)). If an identified SNV was a known variant from dbSNP or 1000 Genome Project, the allele frequencies of CEU, YRI, and CHB/JPT populations from HapMap and 1000 Genome Project were provided. Both SNVs and INDELs were annotated by batch submission to the SeattleSeq server, and for SNVs, additional annotations were acquired using a locally or cloud installed SIFT. The SNVs or INDELs within a user defined distance (default: 5 bases) to exon-intron boundaries were flagged as potential splice variants and the corresponding transcript IDs were provided.
Information was reported on genes hosting SNVs and INDELs, including (i) the KEGG pathway(s) (http://www.genome.jp/kegg) to which the gene belongs; and (ii) tissue expression specificity of the gene.
Table 17 provides the start and end base pair locations for the regions sequenced on chromosomes 1 and 9, respectively.
TABLE 17
Selection of genes for the sequencing analysis.
Chr Start End Chr Start End Size
ATP1B1 1 169,075,947 169,101,960 1 169,065,947 169,609,377 543,430
NME7 1 169,101,771 169,337,186
BLZF1 1 169,337,194 169,365,778
C1orf114 1 169,364,114 169,396,670
SLC19A2 1 169,433,151 169,455,208
F5 1 169,481,192 169,555,769
SELP 1 169,558,090 169,599,377
ABO 9 136,130,563 136,150,630 9 136,120,563 136,160,630 40,067
583,497
Statistical Methods Genome-wide scan (Illumina 660Q; 557,112 SNPs) and candidate gene (n=764 genes relevant to the anticoagulant, procoagulant, fibrinolytic, and innate immunity pathways; n=12,551 SNPs) genotypes from Caucasian VTE cases (objectively-diagnosed; no cancer, catheter or antiphospholipid antibodies; n=1270) and controls (frequency-matched on case age, gender, race, MI/stroke status) were merged and imputed to 2.5 million SNPs with MACH using HapMap Phase 2 (60 CEU; Li et al., Annu. Rev. Genomics Hum. Genet., 10:387-406 (2009)). The primary outcome was VTE status, a binary measure. The covariates were age at interview or blood sample collection, sex, state of residence, and stroke/MI status (Table 10). Association between each SNP and VTE was tested for using unconditional logistic regression, adjusting for age, sex, state of residence, and stroke/MI status using PLINK v 1.07 (Purcell et al., Am. J. Human Genet., 81:559-575 (2007)). Similar analysis was used for the replication analysis, and the covariates were age at interview or blood sample collection, sex and state of residence (Table 11). Novel ABO SNVs were tested for an association with VTE using age-, sex-adjusted logistic regression and Fisher's Exact Test.
TABLE 10
Demographic and clinical characteristics by case-control status
for samples in the discovery data set.
Case Control
Characteristic n = 1503 n = 1459 P-value
Patient age, mean ± SD, years 54.9 ± 16.2 55.6 ± 15.7 0.225
Male, n (%) 745 (49.6) 690 (47.3) 0.216
Stroke or myocardial infarction, 285 (19.0) 150 (10.3) <0.0001
n (%)
U.S. state of residence, n (%) <0.0001
Minnesota 630 (41.9) 811 (55.6)
Other states 873 (58.1) 648 (44.4)
TABLE 11
Significant SNPs with P-values < 10E−05 - adjusted for age, sex, stroke/MI, and U.S. state of residence.
OR Used for
SNP CHR Base Pair MINOR GENE MAF (95% CI) P RSQ IVP GWAS imputation
rs6025 1 167785673 T F5 0.063 3.565 1.68E−22 0.97 TRUE FALSE TRUE
(2.762, 4.602)
rs1894692 1 167734278 G SLC19A2 0.057 3.962 2.85E−21 0.873 FALSE FALSE FALSE
(2.98, 5.268)
rs1018827 1 167780630 A F5 0.106 2.189 4.24E−17 0.981 FALSE FALSE FALSE
(1.824, 2.628)
rs6427196 1 167747847 C F5 0.106 2.174 4.24E−17 0.998 FALSE FALSE FALSE
(1.814, 2.606)
rs6427195 1 167747800 A F5 0.106 2.174 4.28E−17 0.998 FALSE FALSE FALSE
(1.814, 2.606)
rs6427194 1 167747745 T F5 0.106 2.174 4.30E−17 0.998 FALSE FALSE FALSE
(1.814, 2.606)
rs970740 1 167746598 C F5 0.106 2.174 4.35E−17 0.997 FALSE FALSE FALSE
(1.814, 2.606)
rs6687813 1 167744198 A F5 0.104 2.172 6.24E−17 0.997 TRUE FALSE TRUE
(1.811, 2.606)
rs10737547 1 167742676 A F5 0.104 2.173 6.25E−17 0.996 FALSE FALSE FALSE
(1.812, 2.606)
rs6427197 1 167767214 C F5 0.106 2.162 6.92E−17 0.996 FALSE FALSE FALSE
(1.804, 2.591)
rs6009 1 167765458 T F5 0.106 2.16 7.26E−17 0.997 FALSE FALSE FALSE
(1.802, 2.588)
rs2420372 1 167764680 A F5 0.106 2.159 7.47E−17 0.997 FALSE FALSE FALSE
(1.802, 2.587)
rs2420370 1 167757016 G F5 0.106 2.156 8.47E−17 0.998 TRUE FALSE FALSE
(1.799, 2.583)
rs2420371 1 167758179 G F5 0.106 2.151 9.61E−17 0.999 FALSE TRUE TRUE
(1.796, 2.578)
rs649129 9 135144125 T ABO 0.269 1.66 2.94E−16 0.984 FALSE FALSE FALSE
(1.47, 1.874)
rs495828 9 135144688 T ABO 0.272 1.649 2.96E−16 0.988 FALSE TRUE TRUE
(1.462, 1.859)
rs579459 9 135143989 C ABO 0.267 1.662 3.85E−16 0.99 FALSE FALSE FALSE
(1.471, 1.878)
rs2519093 9 135131691 A ABO 0.243 1.685 8.08E−16 NA TRUE FALSE TRUE
(1.484, 1.913)
rs7538157 1 167618168 C BLZF1 0.062 2.685 1.04E−14 0.901 FALSE FALSE FALSE
(2.091, 3.449)
rs651007 9 135143696 T ABO 0.256 1.635 2.20E−14 0.954 FALSE FALSE FALSE
(1.441, 1.855)
rs514659 9 135132024 C ABO 0.405 1.525 6.26E−14 0.999 FALSE FALSE FALSE
(1.366, 1.702)
rs6696217 1 167727350 A SLC19A2 0.133 1.965 6.33E−14 0.822 FALSE FALSE FALSE
(1.647, 2.345)
rs545971 9 135133193 T ABO 0.404 1.525 6.38E−14 0.998 FALSE FALSE FALSE
(1.366, 1.703)
rs612169 9 135133263 G ABO 0.404 1.524 7.21E−14 0.997 FALSE FALSE FALSE
(1.365, 1.701)
rs687289 9 135126927 A ABO 0.404 1.524 7.42E−14 0.999 TRUE FALSE TRUE
(1.365, 1.701)
rs687621 9 135126886 G ABO 0.404 1.523 7.58E−14 0.998 FALSE FALSE FALSE
(1.364, 1.701)
rs674302 9 135136485 A ABO 0.404 1.522 8.14E−14 0.998 FALSE FALSE FALSE
(1.363, 1.699)
rs505922 9 135139050 C ABO 0.403 1.52 9.39E−14 0.999 TRUE TRUE TRUE
(1.361, 1.697)
rs529565 9 135139321 C ABO 0.403 1.52 9.45E−14 0.999 FALSE FALSE FALSE
(1.361, 1.697)
rs1208327 1 167563488 C NME7 0.099 2.04 7.96E−13 0.925 FALSE FALSE FALSE
(1.679, 2.48)
rs643434 9 135132176 A ABO 0.423 1.484 1.16E−12 0.999 TRUE FALSE TRUE
(1.331, 1.654)
rs644234 9 135132038 G ABO 0.423 1.484 1.16E−12 0.999 FALSE FALSE FALSE
(1.331, 1.654)
rs657152 9 135129086 A ABO 0.423 1.483 1.21E−12 0.999 FALSE TRUE TRUE
(1.33, 1.653)
rs16861990 1 167401751 C NME7 0.099 2.019 1.34E−12 0.932 FALSE TRUE TRUE
(1.662, 2.451)
rs8176719 9 135122729 G ABO 0.419 1.469 5.68E−12 NA TRUE FALSE TRUE
(1.317, 1.639)
rs1208135 1 167690722 A SLC19A2 0.09 1.926 4.26E−11 0.93 FALSE FALSE FALSE
(1.585, 2.34)
rs1208134 1 167695568 C SLC19A2 0.09 1.924 4.46E−11 0.933 FALSE TRUE TRUE
(1.584, 2.338)
rs2038024 1 167722606 C SLC19A2 0.177 1.533 1.12E−08 0.893 FALSE TRUE TRUE
(1.324, 1.775)
rs630014 9 135139543 A ABO 0.42 0.736 3.85E−08 0.999 TRUE TRUE TRUE
(0.66, 0.821)
rs633862 9 135145265 C ABO 0.404 0.75 1.68E−07 0.982 FALSE FALSE FALSE
(0.674, 0.836)
rs3756008 4 187422379 T F11 0.418 1.337 2.16E−07 0.952 FALSE FALSE FALSE
(1.198, 1.493)
rs2102575 4 187368498 G CYP4V2 0.1 0.623 3.32E−07 0.98 FALSE TRUE TRUE
(0.519, 0.747)
rs3087505 4 187416480 A KLKB1 0.1 0.628 4.22E−07 0.998 TRUE FALSE TRUE
(0.524, 0.752)
rs12061601 1 167337074 C ATP1B1 0.146 1.508 5.03E−07 0.929 FALSE TRUE TRUE
(1.285, 1.77)
rs2901092 1 167723017 G SLC19A2 0.072 1.872 7.81E−07 0.674 FALSE FALSE FALSE
(1.459, 2.4)
rs925451 4 187424563 A F11 0.413 1.311 8.65E−07 0.994 FALSE TRUE TRUE
(1.177, 1.461)
rs3756009 4 187423105 G F11 0.413 1.312 8.78E−07 0.988 FALSE FALSE FALSE
(1.177, 1.462)
rs11655838 17 5663930 A NLRP1 0.481 1.328 9.68E−07 0.851 FALSE TRUE TRUE
(1.185, 1.487)
rs1877320 4 187368273 G CYP4V2 0.104 0.641 1.02E−06 0.974 FALSE FALSE FALSE
(0.536, 0.766)
rs9995366 4 187368378 T CYP4V2 0.104 0.642 1.12E−06 0.976 FALSE TRUE TRUE
(0.537, 0.767)
rs660340 9 135137374 A ABO 0.408 0.766 1.13E−06 NA TRUE FALSE TRUE
(0.689, 0.853)
rs6842047 4 187370570 A CYP4V2 0.104 0.642 1.16E−06 0.975 FALSE FALSE FALSE
(0.537, 0.768)
rs659104 9 135137644 A ABO 0.408 0.767 1.28E−06 NA TRUE FALSE TRUE
(0.689, 0.854)
rs1799963 11 46717631 A F2 0.025 2.455 1.69E−06 NA TRUE FALSE TRUE
(1.7, 3.546)
rs4253399 4 187425088 G F11 0.411 1.301 1.69E−06 0.996 TRUE TRUE TRUE
(1.168, 1.449)
rs3758348 9 135229220 C SURF4 0.169 1.477 1.79E−06 0.765 FALSE FALSE FALSE
(1.258, 1.733)
rs1323922 13 66385414 G PCDH9 0.12 0.654 2.13E−06 0.842 FALSE TRUE TRUE
(0.549, 0.78)
rs12192563 6 16201441 A MYLIP 0.494 0.763 2.28E−06 0.86 FALSE FALSE FALSE
(0.682, 0.853)
rs9396643 6 16200972 T MYLIP 0.494 0.763 2.28E−06 0.861 FALSE TRUE TRUE
(0.682, 0.853)
rs9358084 6 16200504 G MYLIP 0.494 0.763 2.33E−06 0.86 FALSE FALSE FALSE
(0.682, 0.854)
rs9358083 6 16200051 G MYLIP 0.494 0.763 2.34E−06 0.859 FALSE FALSE FALSE
(0.682, 0.854)
rs7768105 6 16199373 T MYLIP 0.493 0.762 2.39E−06 0.853 FALSE FALSE FALSE
(0.681, 0.853)
rs4716045 6 16204575 T MYLIP 0.489 1.312 2.49E−06 0.861 FALSE FALSE FALSE
(1.172, 1.469)
rs12201671 6 16205941 C MYLIP 0.488 1.311 2.60E−06 0.862 FALSE FALSE FALSE
(1.171, 1.468)
rs6459448 6 16206269 A MYLIP 0.488 1.311 2.66E−06 0.862 FALSE TRUE TRUE
(1.171, 1.467)
rs9383114 6 16207259 A MYLIP 0.488 1.31 2.88E−06 0.861 FALSE FALSE FALSE
(1.17, 1.467)
rs2289252 4 187444375 T F11 0.415 1.316 2.89E−06 0.859 FALSE FALSE FALSE
(1.173, 1.477)
rs6928267 6 16208132 G MYLIP 0.488 1.309 2.94E−06 0.861 FALSE FALSE FALSE
(1.169, 1.466)
rs10949343 6 16209236 C MYLIP 0.494 1.31 2.94E−06 0.852 FALSE FALSE FALSE
(1.17, 1.468)
rs6912988 6 16208633 C MYLIP 0.488 1.309 3.00E−06 0.861 FALSE FALSE FALSE
(1.169, 1.466)
rs12192575 6 16210281 T MYLIP 0.487 1.307 3.34E−06 0.862 FALSE TRUE TRUE
(1.168, 1.463)
rs7745965 6 16210721 A MYLIP 0.487 1.307 3.47E−06 0.86 FALSE FALSE FALSE
(1.167, 1.463)
rs7749877 6 16210781 A MYLIP 0.487 1.307 3.70E−06 0.856 FALSE FALSE FALSE
(1.167, 1.463)
rs10492593 13 66392118 G PCDH9 0.116 0.654 3.82E−06 0.825 FALSE FALSE FALSE
(0.546, 0.783)
rs11832404 12 13897572 C GRIN2B 0.039 0.478 3.94E−06 0.841 FALSE FALSE FALSE
(0.349, 0.654)
rs11833339 12 13899994 G GRIN2B 0.039 0.478 3.95E−06 0.841 FALSE FALSE FALSE
(0.349, 0.654)
rs8176681 9 135129575 C ABO 0.384 0.775 4.15E−06 0.996 FALSE FALSE FALSE
(0.695, 0.864)
rs2073827 9 135126954 C ABO 0.384 0.775 4.34E−06 0.996 FALSE FALSE FALSE
(0.695, 0.864)
rs3917862 1 167859737 G SELP 0.075 1.61 4.35E−06 0.999 TRUE TRUE TRUE
(1.314, 1.972)
rs3134929 6 32300085 G NOTCH4 0.188 0.711 4.43E−06 0.918 FALSE FALSE FALSE
(0.614, 0.822)
rs4253417 4 187435999 C F11 0.427 1.306 4.88E−06 0.86 FALSE FALSE FALSE
(1.165, 1.465)
rs4478991 11 22155841 A TMEM16E 0.436 0.765 5.19E−06 0.828 FALSE FALSE FALSE
(0.681, 0.858)
rs937798 18 60582714 T SERPINB8 0.384 0.77 5.27E−06 0.873 FALSE FALSE FALSE
(0.688, 0.862)
rs11830268 12 13916583 A GRIN2B 0.041 0.498 6.35E−06 0.826 FALSE FALSE FALSE
(0.368, 0.674)
rs11835020 12 13907877 C GRIN2B 0.041 0.499 6.65E−06 0.829 FALSE TRUE TRUE
(0.369, 0.675)
rs12546956 8 18405665 T PSD3 0.115 0.656 7.18E−06 0.767 FALSE FALSE FALSE
(0.545, 0.788)
rs10919168 1 167660850 A C1orf114 0.31 1.317 7.66E−06 0.874 FALSE FALSE FALSE
(1.168, 1.486)
rs3124765 9 135318478 T C9orf7 0.144 1.658 8.44E−06 0.454 FALSE FALSE FALSE
(1.327, 2.071)
rs4244490 11 22135551 A TMEM16E 0.427 0.771 8.70E−06 0.84 FALSE FALSE FALSE
(0.687, 0.865)
rs4275631 11 22138940 T TMEM16E 0.427 0.771 8.70E−06 0.844 FALSE FALSE FALSE
(0.688, 0.865)
rs4962153 9 135313575 A ADAMTS13 0.165 1.52 9.10E−06 0.586 FALSE FALSE FALSE
(1.264, 1.829)
rs9323164 14 48222321 T RPS29 0.409 0.771 9.12E−06 0.853 FALSE FALSE FALSE
(0.688, 0.865)
rs739468 9 135316069 T C9orf7 0.165 1.523 9.28E−06 0.582 FALSE FALSE FALSE
(1.264, 1.833)
rs12029857 1 167417852 C NME7 0.114 1.617 9.39E−06 0.656 FALSE FALSE FALSE
(1.307, 2)
rs1557570 1 167774468 T F5 0.325 0.772 9.51E−06 0.939 FALSE FALSE FALSE
(0.688, 0.866)
rs17490626 10 70888652 C TSPAN15 0.119 0.673 9.56E−06 0.825 FALSE FALSE FALSE
(0.565, 0.802)
rs7481951 11 22228446 A TMEM16E 0.42 0.773 9.59E−06 0.852 FALSE FALSE FALSE
(0.689, 0.866)
rs1563455 4 190530151 T FRG1 0.248 0.714 9.98E−06 0.671 FALSE FALSE FALSE
(0.615, 0.829)
URLs PLINK, http://pngu.mgh.harvard.edu/˜purcell/plink/; public sequence primers,
- http://genetics.uiowa.edu; Phred, Phrap, Consed,
- http://www.phrap.org/phredphrapconsed.html; PolyPhred,
- http://droog.gs.washington.edu/polyphred/; PolyPhen,
- http://genetics.bwh.harvard.edu/pph/.
Results Results from a merged GWAS and candidate gene genotyping study with additional genotypes from imputation using a larger sample size of U.S. VTE cases of non-Hispanic European-ancestry, and U.S. controls frequency-matched on age and gender were obtained (Table 10). From population stratification analysis, 98.64% of samples were classified as European and 1.36% as “other” ancestry (includes individuals of mixed ancestry; FIG. 14).
After adjusting for age, gender, U.S. state of residence, and stroke/MI status, 39 SNPs exceeded genome-wide significance of 5×10E-8 (FIG. 15 and Table 11); F2 rs1799963 (Prothrombin G20210A) was borderline significant (OR=2.46, p=1.7E-06). Table 12 shows the association results for significant SNPs not in linkage disequilibrium within a gene (F5 rs6025, BLZF1 rs7538157, NME7 rs16861990, SLC19A2 rs2038024, and ABO rs2519093, rs8176719 [blood group non-O] and rs495828). BLZF1 rs7538157 was in high linkage disequilibrium (LD) with F5 rs6025, SLC19A2 rs2038024, and ATP1B1 rs12061601. In a replication study (Table 13), adjusted for age, gender and U.S. state of residence, F5 rs6025 (p=1.4E-12), NME7 rs16861990 (p=4.9E-9), ATP1B1 rs12061601 (p=0.02), ABO rs2519093 (p=1.2E-17), rs495828 (p=2.4E-17), and rs8176719 (p=5.7E-16), and F2 rs1799963 were significantly associated with VTE, and SLC19A2 rs2038024 (p=0.09) was marginally associated (Table 14). All replicated SNP ORs were in the same direction and of similar magnitude as that of the GWAS.
TABLE 12
Odds ratio and 95% confidence intervals, minor allele, minor allele frequency (MAF)
and imputation quality for single nucleotide polymorphisms (SNPs) showing genome-
wide significance, adjusted for age, gender, stroke/MI and state of residence.
Minor Imputed (r2)/
SNP Chr Position† allele Gene MAF OR (95% CI) P-value Genotype
SNPs in genes previously reported
rs6025 1 167785673 T F5 0.063 3.57 (2.76, 4.60) 1.68E−22 Yes (0.97)/Yes
rs8176719 9 135122729 G ABO 0.419 1.47 (1.32, 1.64) 5.68E−12 No/Yes‡
rs2519093 9 135131691 A ABO 0.243 1.69 (1.48, 1.91) 8.08E−16 No/Yes‡
SNPs in genes not previously reported
rs7538157 1 167618168 C BLZF1 0.062 2.69 (2.09, 3.45) 1.04E−14 Yes (0.901)/No
rs16861990 1 167401751 C NME7 0.099 2.02 (1.66, 2.45) 1.69E−12 Yes (0.932)/Yes§
rs2038024 1 167722606 C SLC19A2 0.177 1.53 (1.32, 1.78) 1.12E−08 Yes (0.893)/Yes§
rs495828 9 135144688 T ABO 0.272 1.65 (1.46, 1.86) 2.96E−16 Yes (0.988)/Yes§
†NCBI build 36 of the human genome
‡Genotype available in all subjects through the candidate gene data set.
§Genotype available in only 2570 subjects (87% of our combined samples) through the GWA data set
TABLE 13
Demographic characteristics by case-control status for samples
in the replication data set.
Cases Controls
Characteristics n = 1407 n = 1418 Total
Patient age, mean ± SD, years 60.8 ± 16.7 64.9 ± 12.8 62.9 ± 15.0
Male, n (%) 47.1 48.0 47.4
Olmsted County, MN 52.4 51.7 52.0
resident, n (%)
Minnesota residents, n (%) 67.2 70.7 69.0
TABLE 14
Replication odds ratio and 95% confidence intervals, minor allele, minor allele
frequency (MAF; overall and by case/control status) using 2,825 subjects (1407
cases and 1418 controls), adjusted for age, gender and U.S. state of residence.
SNP Gene N MAF MAF - cases MAF - controls OR (95% CI) P value
rs6025 F5 2543 0.059 0.085 0.034 2.6 (2.0, 3.3) 1.40E−12
rs16861990 NME7 2559 0.095 0.122 0.069 1.8 (1.5, 2.2) 4.94E−09
rs12061601 ATP1B1 2521 0.140 0.154 0.127 1.2 (1.0, 1.4) 0.02
rs2038024 SLC19A2 2603 0.171 0.182 0.159 1.1 (1.0, 1.3) 0.09
rs2519093 ABO 2599 0.234 0.286 0.183 1.8 (1.6, 2.1) 1.17E−17
rs495828 ABO 2627 0.260 0.314 0.207 1.7 (1.5, 2.0) 2.41E−17
rs8176719 ABO 2532 0.415 0.472 0.357 1.6 (1.5, 1.8) 5.68E−16
rs1799963 F2 2620 0.020 0.024 0.015 1.6 (1.1, 2.4) 0.03
These SNPs cluster in two genomic regions located on chromosome 1q (FIG. 16A) and on chromosome 9q (FIG. 16B). Since NME7, ATP1B1, SLC19A2, BLZF1, SELL, and SELP are in close proximity to F5, the association analysis including F5 rs6025 (Factor V Leiden) as a covariate was repeated, and only the ABO SNPs remained significantly associated with VTE at the genome-wide level. Similarly, in the replication study, only the ABO SNPs remained statistically significant after adjusting for F5 rs6025 (Table 15). Receiver Operating Characteristic (ROC) areas under the curve (AUC), calculated individually and jointly using all significant SNPs, were not appreciably different for covariates plus F5 rs6025 (AUC=0.653) vs. covariates plus F5 rs6025, NME7 rs16861990, BLZF1 rs7538157 vs. ATP1B1 rs12061601 and SLC19A2 rs2038024 (AUC=0.654).
TABLE 15
Replication odds ratio and 95% confidence intervals using
2,825 subjects (1407 cases and 1418 controls), adjusted for
age, gender, U.S. state of residence and F5 rs6025 (Factor V Leiden).
SNP Gene N OR (95% CI) P value
rs16861990 NME7 2631 1.2 (0.9, 1.6) 0.13
rs12061601 ATP1B1 2605 0.9 (0.8, 1.1) 0.52
rs2038024 SLC19A2 2601 0.8 (0.7, 1.0) 0.01
rs2519093 ABO 2601 1.8 (1.6, 2.1) 3.2E−17
rs495828 ABO 2629 1.7 (1.5, 2.0) 8.91E−17
rs8176719 ABO 2603 1.6 (1.4, 1.8) 1.97E−13
rs1799963 F2 2609 1.7 (1.1, 2.5) 0.02
To further evaluate ABO sequence variation for an association with VTE, ABO deep sequencing including 10 Kb of the flanking regions using Illumina HiSeq 2000 was performed. Excluding the intronic repeat regions, 98% of the targeted area was sequenced with >20× coverage in 96 samples (82 VTE cases and 14 controls). On average, ˜600 SNVs and ˜50 INDELs were detected in each sample. Fifteen novel single nucleotide variations (SNVs) in ABO intron 6 and the ABO 3′ UTR were associated with VTE (p<E-06) and belonged to three distinctive LD blocks; none were in LD with ABO rs8176719 or rs2519093 (Table 16). SNVs inside the middle LD block at the 3′ of ABO were located within an enhancer and promoter histone marked with putative transcription factor binding sites. In addition, strong evidence from both ENCODE and dbEST supported the middle LD block as lying within a novel transcript, probably an extension of the 3′ of ABO. In addition, a novel, significant, protective, frame-shifting single base (G) deletion was discovered at ABO chr9:135120877.
TABLE 16
Summary of the significant SNVs.
MAF, N MAF, N MAF, N MAF, N MAF, N
Major Minor Controls Controls Cases Cases Cases
Position Genomic Location Allele Allele 1/0 2/1 0/0 1/1 2/2 P-value
135111124† 10 kb 3′ of ABO C T 0.30, 10 0.38, 4 0.04, 28 0.02, 27 0.02, 27 3.78E−07
135111447 10 kb 3′ of ABO G A 0.30, 10 0.38, 4 0.02, 28 0.00, 27 0.02, 27 2.43E−08
135111473 10 kb 3′ of ABO A G 0.35, 10 0.50, 4 0.05, 28 0.04, 27 0.02, 27 1.05E−08
135112074 9 kb 3′ of ABO T C 0.30, 10 0.38, 4 0.04, 28 0.02, 27 0.02, 27 3.78E−07
135112527 9 kb 3′ of ABO T C 0.35, 10 0.50, 4 0.05, 28 0.04, 27 0.02, 27 1.05E−08
135116452 4 kb 3′ of ABO C A 0.15, 10 0.50, 4 0.02, 28 0.02, 27 0.00, 27 2.74E−06
135117089‡ 4 kb 3′ of ABO T C 0.30, 10 0.00, 4 0.00, 28 0.02, 27 0.02, 27 4.02E−05
135117302 3 kb 3′ of ABO A G 0.30, 10 0.00, 4 0.00, 28 0.00, 27 0.02, 27 6.35E−06
135117426 3 kb 3′ of ABO C G 0.28, 9 0.00, 4 0.00, 28 0.00, 27 0.00, 26 3.80E−06
135117777 3 kb 3′ of ABO A C 0.30, 10 0.00, 4 0.00, 28 0.00, 27 0.02, 27 6.35E−06
135121716§ ABO intron 6 C T 0.11, 9 0.00, 4 0.02, 28 0.00, 27 0.00, 27 4.76E−05
135121989 ABO intron 6 T C 0.15, 10 0.50, 3 0.02, 28 0.00, 27 0.00, 27 6.00E−07
135122337 ABO intron 6 G A 0.11, 9 0.50, 4 0.02, 28 0.00, 27 0.00, 27 4.21E−06
135122346 ABO intron 6 T C 0.15, 10 0.50, 4 0.02, 28 0.00, 27 0.00, 27 6.00E−07
135122575 ABO intron 6 C A 0.15, 0.50 0.02 0 0 6.00E−07
†LD block (r2 = 0.62-0.83)
‡LD block (r2 > 0.80)
§LD block (r2 > 0.85)
None of the significant SNVs are in high LD with the two SNPs used to select cases and controls (rs8176719 and rs2519093).
These results demonstrate that SNVs within three ABO LD blocks are significantly associated with VTE.
Other Embodiments It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
